Antibodies to EphA3

ABSTRACT

The current invention relates to high-affinity antibodies to EphA3 that have reduced immunogenicity when administered to a human to treat diseases and method of using such antibodies.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of application Ser. No. 12/904,953,filed Oct. 14, 2010, which claims benefit of U.S. provisionalapplication No. 61/251,668, filed Oct. 14, 2009. Each application isherein incorporated by reference.

REFERENCE TO A “SEQUENCE LISTING,” SUBMITTED AS AN ASCII TEXT FILE

The Sequence Listing written in file SEQTXT_(—)87142-896750.txt, createdon Dec. 27, 2013, 77,099 bytes, machine format IBM-PC, MS-Windowsoperating system, is incorporated by reference for all purposes.

BACKGROUND OF THE INVENTION

Eph receptor tyrosine kinases (Ephs) belong to a large group of receptortyrosine kinases (RTKs), kinases that phosphorylate proteins on tyrosineresidues. Ephs and their membrane bound ephrin ligands (ephrins) controlcell positioning and tissue organization (Poliakov, A., et al., Dev Cell7:465-80 (2004)). In contrast to other receptor tyrosine kinases, Ephreceptor activation does not only require ligand binding anddimerization but also involves preformed ligand oligomers. Thus,tyrosine phosphorylation of Eph receptors requires presentation ofephrin ligands in their clustered or membrane-attached forms (Davis etal., Science 266:816-819 (1994)). Functional and biochemical Ephresponses occur at higher ligand oligomerization states (Stein et al.,Genes Dev 12:667-678 (1998)).

Among other patterning functions, various Ephs and ephrins have beenshown to play a role in vascular development. The de-regulatedre-emergence of some ephrins and their receptors in adults also has beenobserved to contribute to tumor invasion, metastasis andneo-angiogenesis. For example, dominant-negative, soluble EphA2 or A3proteins exhibit effects on ephrin-induced endothelial cell function invitro, and tumor angiogenesis and progression in vivo (Nakamoto, et al.,Microsc Res Tech 59:58-67 (2002); Brantley-Sieders, et al., Curr PharmDes 10:3431-42 (2004); Brantley, et al. Oncogene 21:7011-26 (2002);Cheng, et al. Neoplasia 5:445-56 (2003). Dobrzanski, et al. Cancer Res64:910-9 (2004)). Furthermore, Eph family members have been found to beover-expressed on tumor cells from a wide variety of human solid tumors(Brantley-Sieders, et al., Curr Pharm Des 10:3431-42 (2004); Marme, D.Ann Hematol 81 Suppl 2:S66 (2002); Booth, C. et al., Nat Med 8:1360-1(2002)).

Epha3 has also been reported to be activated and overexpressed on CD34⁺cells in chronic myeloid leukemia (CML) patients in the acceleratedphase and blast crisis stage (Cilloni et al., American Society ofHematology, Abstract 1092, 2008 (available on line Nov. 14, 2008)).Cilloni et al. reported that when primary CML cells or EphA3-transfectednormal cells were incubated with a specific monoclonal antibody, theantibody induced a significant reduction of proliferation in primarycells and transfected cells, reduced colony growth and induced changesto the adhesion properties. The antibody did not induce any significantchanges in normal control cells or cells from CML patient in the chronicstage.

This invention is based, in part, on the discovery of new anti-EphA3antibodies.

BRIEF SUMMARY OF THE INVENTION

The invention is directed to potent anti-EphA3 antibodies and methods ofusing such antibodies, e.g., for the treatment of a disease involvingEphA3. An antibody of the invention has the characteristics as describedherein. Thus, in one aspect, an antibody of the invention comprises aV_(H) region that comprises a CDR3 comprising the amino acid sequenceX₁GX₂YEX₃FDX₄ _(—) (SEQ ID NO:38), wherein X₁ is S or G, X₂ is Y or V,X₃ is E or D, and X₄ is 5, V, or I, with the proviso that when the aminoacid sequence is SGYYEDFDS (SEQ ID NO:39) the CDR1 is not SYWIN (SEQ IDNO:40) and when the amino acid sequence is SGYYEEFDS (SEQ ID NO:41) theCDR1 is not TYWIS (SEQ ID NO:42). In some embodiments, the antibody hasa CDR3 that comprises the amino acid sequence GGYYEDFDS (SEQ ID NO:43),SGYYEEFDS (SEQ ID NO:41), SGVYEDFDS (SEQ ID NO:44), SGYYEDFDV (SEQ IDNO:45), or SGYYEDFDI (SEQ ID NO:46). In some embodiments, the antibodyhas a J segment that comprises at least 80% identity, typically at 85%,or at least 90% identity, to a human germline J segment amino acidsequence; or that differs from a human germline J segment at no morethan two positions; and a V-segment that comprises at least 80%identity, typically at least 85% identity, and preferably 90% identity,or greater, to a human germ line V-segment amino acid sequence. In someembodiment, the J segment comprises at least 90% identity to human JH6amino acid sequence, and the V-segment comprises at least 90% identityto a human VH1 1-02 amino acid sequence. In some embodiments, theantibody has an FR4 that comprises WGQGTTVTVSS (SEQ ID NO:47), or an FR4that differs no more than one amino acid from WGQGTTVTVSS (SEQ IDNO:47). In some embodiments, the antibody comprises a V_(H) CDR1, or aV_(H) CDR2, or both a V_(H) CDR1 and a V_(H) CDR2, as shown in a V_(H)region set forth in FIG. 1. For example, an antibody of the inventioncan have a V_(H) CDR1 that has the amino acid sequence GYWMN (SEQ IDNO:48), TYWIS (SEQ ID NO:42), or SYWIN (SEQ ID NO:40) and/or a CDR2 thathas the amino acid sequence DIYPGSGNTNYDEKFQG (SEQ ID NO:49),DIYPGSGNTNYAQKFQG (SEQ ID NO:50), DIYPGSGNTNYAQEFRG (SEQ ID NO:51),DIYPGSGNTNYAQKFLG (SEQ ID NO:52), DIYPGSGNTNYDEKFEG (SEQ ID NO:53), orDIYPGSGNTNYDEKFKR (SEQ ID NO:54). In some embodiments, the antibody hasa V_(H) CDR1 GYWMN (SEQ ID NO:48) and a CDR2 DIYPGSGNTNYDEKFQG (SEQ IDNO:49). In some embodiments, the antibody has a V_(H) CDR1 TYWIS (SEQ IDNO:42) and a V_(H) CDR2 DIYPGSGNTNYAQ(K/E)F(Q/R/L)G (SEQ ID NO:55). Insome embodiments, an antibody of the invention has the V_(H) CDR1, CDR2,and CDR3 from one of the V regions as shown in FIG. 1. In someembodiments, the antibody has a V_(H) V-segment amino acid sequence of aV-segment sequence shown in FIG. 1. In some embodiments, the V_(H) hasthe sequence of a V_(H) region set forth in FIG. 1.

The invention also provides an antibody that has a V_(L) region thatcomprises a CDR3 binding specificity determinant having the sequenceX₁X₂YX₃X₄YPYT (SEQ ID NO:56), wherein X₁ is G, V, or A; X₂ is Q, R, orG; X₃ is A, S, or L; and X₄ is N or K. In some embodiments, the CDR3comprises GQYANYPYT (SEQ ID NO:57), VQYAKYPYT (SEQ ID NO:58), AQYANYPYT(SEQ ID NO:59), VQYSNYPYT (SEQ ID NO:60), VQYANYPYT (SEQ ID NO:61),VGYANYPYT (SEQ ID NO:62), VRYANYPYT (SEQ ID NO:63), or VQYLNYPYT (SEQ IDNO:64). In some embodiments, when the CDR3 is VQYANYPYT (SEQ ID NO:61),the CDR1 is not RASQEISGYLG (SEQ ID NO:65), or RASQGIISYLA (SEQ IDNO:66) and/or the CDR2 is not AASTLDS (SEQ ID NO:67) or AASSLQS (SEQ IDNO:68). In some embodiments, the V_(L) region comprises a J segment thatcomprises at least 80% identity, typically at least 85% or 90% identity,to a human germline J segment amino acid sequence, or that differs nomore than two amino acids from a human germline segment; and a V-segmentthat comprises at least 80% identity, typically at least 90% identity,or greater, to a human germ line V-segment amino acid sequence. In someembodiments, the J segment has no more than two amino acid changes,often no more than one amino acid change, relative to the sequenceFGQGTKLEIK (SEQ ID NO:69) from the human germ-line Jκ2 amino acidsequence and the V-segment comprises at least 90% identity to humangermline JκI L15 amino acid sequence. In some embodiments, the FR4 ofthe antibody has the amino acid sequence FGQGTKLEIK (SEQ ID NO:69), orhas no more than one amino acid residue changed relative to the sequenceFGQGTKLEIK (SEQ ID NO:69). In some embodiments, the V_(L) regioncomprises a CDR1, or a CDR2, or both a CDR1 and CDR2 of a sequence VLregion shown in FIG. 1. For example, a CDR1 can have the sequenceRASQGIISYLA (SEQ ID NO:66), QASQDISTYLN (SEQ ID NO:70), RASQEISGYLG (SEQID NO:65), or RASQSISSYLA (SEQ ID NO:71); and/or a CDR2 can have thesequence AASSLQS (SEQ ID NO:68), GASSLQS (SEQ ID NO:72), AASSLQR (SEQ IDNO:73), or AASTLDS (SEQ ID NO:67). In some embodiments, the CDR1 has thesequence RASQGIISYLA (SEQ ID NO:66) and the CDR2 has the sequenceGASSLQS (SEQ ID NO:72). In some embodiments, the CDR1 has the sequenceQASQDISTYLN (SEQ ID NO:70) and the CDR2 has the sequence AASSLQR (SEQ IDNO:73) or AASSLQS (SEQ ID NO:68). In some embodiments, the CDR1 has thesequence RASQSISSYLA (SEQ ID NO:71) and the CDR2 has the sequenceAASSLQR (SEQ ID NO:73). In some embodiments, the V_(L) region comprisesthe CDR1, CDR2, and CDR3 of one of the V_(L) regions set forth inFIG. 1. In some embodiments, the V_(L) region comprises a V-segment thathas a V-segment sequence as shown in FIG. 1. In some embodiments, theV_(L) region has the sequence of a V_(L) region set forth in FIG. 1. Intypical embodiments, the V_(H) region of the antibody comprises any ofthe V_(H) regions described in the preceding paragraph.

In some embodiments, the invention provide an antibody that comprises aV_(L) region that has a CDR3 comprising GQYANYPYT (SEQ ID NO:57),VQYAKYPYT (SEQ ID NO:58), AQYANYPYT (SEQ ID NO:59), VQYSNYPYT (SEQ IDNO:60), VGYANYPYT (SEQ ID NO:61), VRYANYPYT (SEQ ID NO:63), or VQYLNYPYT(SEQ ID NO:64). In some embodiments, the antibody comprises a heavychain CDR3 comprising the amino acid sequence X₁GX₂YEX₃FDX₄ (SEQ IDNO:38), wherein X₁ is S or G, X₂ is Y or V, X₃ is E or D, and X₄ is 5,V, or I. In some embodiments. In some embodiments, the heavy chain CDR3comprises the amino acid sequence GGYYEDFDS (SEQ ID NO:43), SGYYEEFDS(SEQ ID NO:41), SGVYEDFDS (SEQ ID NO:44), SGYYEDFDV (SEQ ID NO:45), orSGYYEDFDI (SEQ ID NO:46). In some embodiments, the antibody comprises alight chain CDR1 or CDR2 set forth in FIG. 1, or a heavy chain CDR1 orCDR2 set forth in FIG. 1. In some embodiments, the antibody comprises alight chain CDR1 and CDR2 as set forth in FIG. 1 and/or a heavy chainCDR1 and CDR2 set forth in FIG. 1. In some embodiments, the antibodycomprises a V_(L) V-segment set forth in FIG. 1.

The invention additionally provides an antibody that comprises a V_(H)region comprising a CDR3 having the sequence SGYYE(E/D)FDS (SEQ IDNO:74) and a V_(L) region CDR3 sequence set forth in the precedingparagraph, with the proviso that the V_(L) region CDR3 sequence is notVQYANYPYT (SEQ ID NO:61) or VQYMNYPYT (SEQ ID NO:75). In someembodiments, the antibody comprises a heavy chain CDR1 or CDR2 set forthin FIG. 1, or a light chain CDR1 or CDR2 set forth in FIG. 1. In someembodiments, the antibody comprises a heavy chain CDR1 and CDR2 as setforth in FIG. 1 and/or a light chain CDR1 and CDR2 set forth in FIG. 1.

In some embodiments, an anti-EphA3 antibody of the invention comprisesthe V_(H) CDR1, CDR2, and CDR3 from one of the V_(H) regions set forthin FIG. 1 and the V_(L) CDR1, CDR2, and CDR3 from one of the V_(L)regions set forth in FIG. 1.

An antibody of the invention can comprise a V_(H) region as set forth inFIG. 1 or a V_(L) region as set forth in FIG. 1. Often, the antibodycomprises a V_(H) region as set forth in FIG. 1 and a V_(L) region asset forth in FIG. 1. In some embodiments, the antibody comprises acombinations of V_(H) and V_(L) regions that comprise: a) SEQ ID NO:1and SEQ ID NO:20, b) SEQ ID NO:2 and SEQ ID NO:11, c) SEQ ID NO: 2 andSEQ ID NO:12, d) SEQ ID NO:2 and SEQ ID NO:19, e) SEQ ID NO:2 and SEQ IDNO:21, f) SEQ ID NO:2 and SEQ ID NO:22, g) SEQ ID NO:2 and SEQ ID NO:23,h) SEQ ID NO:3 and SEQ ID NO:11, i) SEQ ID NO:3 and SEQ ID NO:12, j) SEQID NO:3 and SEQ ID NO:21, k) SEQ ID NO:3 and SEQ ID NO:22, l) SEQ IDNO:4 and SEQ ID NO:11, m) SEQ ID NO:4 and SEQ ID NO:13, n) SEQ ID NO:5and SEQ ID NO:11, o) SEQ ID NO:5 and SEQ ID NO:13, p) SEQ ID NO:5 andSEQ ID NO:21, q) SEQ ID NO:6 and SEQ ID NO:14, r) SEQ ID NO:6 and SEQ IDNO:15, s) SEQ ID NO:7 and SEQ ID NO:14, t) SEQ ID NO:7 and SEQ ID NO:15,u) SEQ ID NO:8 and SEQ ID NO:14, v) SEQ ID NO:8 and SEQ ID NO:15, w) SEQID NO:9 and SEQ ID NO:16, x) SEQ ID NO:9 and SEQ ID NO:17, y) SEQ IDNO:9 and SEQ ID NO:19, z) SEQ ID NO:10 and SEQ ID NO:17, aa) SEQ IDNO:10 and SEQ ID NO:18, or bb) SEQ ID NO:10 and SEQ ID NO:20.

In some embodiments, an antibody of the invention, e.g., that has aV_(H) region sequence selected from the V_(H) region sequences in FIG. 1and a V_(L) region selected from the V_(L) region sequences in FIG. 1,has a monovalent affinity better than about 10 nM, and often better thanabout 5 nM or 1 nM as determined by surface plasmon resonance analysisperformed at 37° C. Thus, in some embodiments, the antibodies of theinvention have an affinity (as measured using surface plasmon resonance)of about 10 nM, about 5 nM, about 2.5 nM, about 1 nM, about 0.5 nM,about 0.25 nM, or about 0.1 nM, or better.

An antibody of the invention as described herein may have a V_(H) regionand/or a V_(L) region that comprises a methionine at the N-terminus

In some embodiments, the antibody is an IgG. In some embodiments, theantibody is an IgG1 or an IgG3. In some embodiments, the antibody is anIgG2 or an IgG4.

In some embodiments, the antibody comprises a heavy chain constantregions having the amino acid sequence set forth in SEQ ID NO:24 and/ora kappa light chain constant region having the amino acid sequence setforth in SEQ ID NO:25.

In some embodiments, the heavy chain constant region of an antibody isafucosylated. In some embodiments, an antibody preparation comprising anantibody of the invention is hypofucosylated or afucosylated.

In some embodiments, an anti-EphA3 antibody of the invention has a heavychain amino acid sequence and a light chain amino acid sequence thatcomprises SEQ ID NO:26 and SEQ ID NO:27, SEQ ID NO:28 and SEQ ID NO:29,SEQ ID NO:30 and SEQ ID NO:31, SEQ ID NO:32 and SEQ ID NO:33, SEQ IDNO:34 and SEQ ID NO:35, or SEQ ID NO:36 and SEQ ID NO:27, respectively;and the antibody is afucosylated.

In some embodiments, the antibody is a (Fab′)₂.

In some embodiments the antibody is PEGylated.

In some embodiments, the antibody activates EphA3.

In some embodiments, the antibody does not compete with a naturalligand, e.g., ephrin A5, for binding to EphA3.

In another aspect, the invention provides a method of treating a patientthat has an EphA3-dependent disease, the method comprising administeringan antibody of the invention as described herein to the patient in atherapeutically effective amount. The patient may, e.g., have a cancer.In some embodiments, the antibody is administered to a patient that hasa solid tumor that comprises tumor cells that express EphA3. In otherembodiments, the antibody is administered to a patient that as a tumorthat does not have tumor cells that express EphA3.

In some embodiments, the antibody is administered to a patient that hasa myeloproflierative disorder. In some embodiments, the antibody isadministered to a patient that has acute myeloid leukemia or chronicmyeloid leukemia. In some embodiments, the antibody is administered to apatient that has a lymphoma. In some embodiments, the antibody isadministered to a patient that has myelodysplastic syndrome,polycythemia vera, essential thrombocythemia, or idiopathicmyelofibrosis.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides exemplary V_(H) (SEQ ID NOS:1-10) and V_(L) (SEQ IDNOS:11-23) sequences of anti-EphA3 antibodies of the invention

FIG. 2 provides a schematic of a heavy chain CDR2/FR3 cassetteconstruction (SEQ ID NOS:54, 76 and 77).

FIG. 3 shows results of an antigen binding ELISA with anti-EphA3 IgGs.ELISA plates coated with EphA3-Fc were treated with chimeric IIIA4(circles), an exemplary engineered antibody of the invention (squares)or a control IgG (triangles) and probed for binding with an anti-humankappa chain HRP conjugate.

FIG. 4 shows the specificity of an engineered antibody of the inventionfor EphA3. Various Eph proteins were coated onto an ELISA plate, treatedwith engineered antibody and probed for binding with an anti-human kappachain HRP conjugate.

FIG. 5 shows data from flow cytometric analysis of three cell lines inan experiment evaluated the ability of an exemplary engineeredanti-EphA3 antibody of the invention to bind to cell surface expressedEphA3. B16, SKme128, and LnCAP cells were blocked with 2% BSA and ratIgG and probed with engineered anti-EphA3 IgG, chimeric IIIA4 IgG or anisotype control IgG. Bound antibody was detected by an anti-human IgGPhycoerythrin conjugate using a Facs Caliber flow cytometry (BD). Deadcells were excluded by propidium iodide staining. For each graph, thecontrol antibody profile is the left-most curve shown in the graph.

FIG. 6 provides data showing that an afucosylated anti-EphA3 antibodyhas enhanced ADCC activity against AML cells compared with thefucosylated anti-EphA3 antibody.

DETAILED DESCRIPTION OF THE INVENTION

As used herein “EphA3” refers to the Eph receptor A3. This receptor hasalso been referred to as “Human embryo kinase”, “hek”, “eph-liketyrosine kinase 1”, “etk1” or “tyro4”. EphA3 belongs to the ephrinreceptor subfamily of the protein-tyrosine kinase family. EPH andEPH-related receptors have been implicated in mediating developmentalevents. Receptors in the EPH subfamily typically have a single kinasedomain and an extracellular region containing a Cys-rich domain and 2fibronectin type III repeats. The ephrin receptors are divided into 2groups based on the similarity of their extracellular domain sequencesand their affinities for binding ephrin-A and ephrin-B ligands. EphA3binds ephrin-A ligands. EphA3 nucleic acid and protein sequences areknown. An exemplary human EphA3 amino acid sequence is available underaccession number (EAW68857).

In the present invention, “activation” of EphA3 causes phosphorylationof EphA3. An antibody that activates EphA3, i.e., causes phosphorylationof EphA3, is therefore considered to be an agonist in the context ofthis invention. EphA3 can be activated by dimerization. Such activationcan lead to phosphorylation and apoptosis, although not necessarily tocell rounding. Activation, e.g., when clustering of EphA3 occurs, canadditionally lead to morphological changes, typically rounding of thecell.

In the present invention, “EphA3 antibody” or “anti-EphA3 antibody” areused interchangeably to refer to an antibody that specifically binds toEphA3. In some embodiments, the antibody can dimerize EphA3. The termencompasses antibodies that bind to EphA3 in the presence of ephrinligand (e.g., ephrin A5) binding, as well as antibodies that bind to theligand binding site and compete with ligand binding to EphA3.

An “EphA3 antibody that binds to EphA3 in the presence of binding of anephrin ligand” refers to an antibody that does not significantly preventbinding of an ephrin ligand, such as ephrin A5, to EphA3. The presenceof such an antibody in a binding reaction comprising EphA3 and an ephrinligand, e.g., ephrin A5, reduces ephrin ligand binding to EphA3 by lessthan about 30%, typically less than 20% or 10%.

The term “mAb IIIA4” refers to monoclonal antibody IIIA4 that wasoriginally raised against LK63 human acute pre-B leukemia cells toaffinity isolate EphA3 (Boyd, et al. J Biol Chem 267:3262-3267, 1992).mAb IIIA4 binds to the native EphA3 globular ephrin-binding domain(e.g., Smith, et al., J. Biol. Chem 279:9522-9531, 2004). It isdeposited in the European Collection of Animal Cell Cultures underaccession no. 91061920 (see, e.g., EP patent no. EP0590030).

An “antibody having an active isotype” as used herein refers to anantibody that has a human Fc region that binds to an Fc receptor presenton immune effector cells. “Active isotypes” include IgG1, IgG3, IgM,IgA, and IgE. The term encompasses antibodies that have a human Fcregion that comprises modifications, such as mutations or changes to thesugar composition and/or level of glycosylation, that modulate Fceffector function.

An “Fc region” refers to the constant region of an antibody excludingthe first constant region immunoglobulin domain. Thus, Fc refers to thelast two constant region immunoglobulin domains of IgA, IgD, and IgG,and the last three constant region immunoglobulin domains of IgE andIgM, and the flexible hinge N-terminal to these domains. For IgA and IgMFc may include the J chain. For IgG, Fc comprises immunoglobulin domainsCγ2 and Cγ3 and the hinge between Cγ1 and Cγ. It is understood in theart that the boundaries of the Fc region may vary, however, the humanIgG heavy chain Fc region is usually defined to comprise residues C226or P230 to its carboxyl-terminus, using the numbering is according tothe EU index as in Kabat et al. (1991, NIH Publication 91-3242, NationalTechnical Information Service, Springfield, Va.). The term “Fc region”may refer to this region in isolation or this region in the context ofan antibody or antibody fragment. “Fc region” includes naturallyoccurring allelic variants of the Fc region as well as modificationsthat modulate effector function. Fc regions also include variants thatdon't result in alterations to biological function. For example, one ormore amino acids can be deleted from the N-terminus or C-terminus of theFc region of an immunoglobulin without substantial loss of biologicalfunction. Such variants can be selected according to general rules knownin the art so as to have minimal effect on activity (see, e.g., Bowie,et al., Science 247:306-1310, 1990).

The term “equilibrium dissociation constant” or “affinity” abbreviated(K_(D)), refers to the dissociation rate constant (k_(d), time⁻¹)divided by the association rate constant (k_(a), time M⁻¹). Equilibriumdissociation constants can be measured using any known method in theart. The antibodies of the present invention are high affinityantibodies. Such antibodies have a monovalent affinity better (less)than about 50 nM and often less than about 10 nM as determined bysurface plasmon resonance analysis performed at 37° C. Thus, in someembodiments, the antibodies of the invention have an affinity (asmeasured using surface plasmon resonance) of less than about 50 nM,typically less than about 25 nM, or even less than 10 nM, e.g., about 5nM or about 1 nM. In the context of the invention, an affinity is“better” if it has a higher affinity, e.g., as evidenced by a lowernumerical K_(D).

The phrase “specifically (or selectively) binds” to an antibody or“specifically (or selectively) immunoreactive with,” when referring to aprotein or peptide, refers to a binding reaction where the antibodybinds to the protein of interest. In the context of this invention, theantibody typically binds to EphA3 with an affinity that is at least100-fold greater than its affinity for other antigens.

As used herein, an “antibody” refers to a protein functionally definedas a binding protein and structurally defined as comprising an aminoacid sequence that is recognized by one of skill as being derived fromthe framework region of an immunoglobulin encoding gene of an animalproducing antibodies. An antibody can consist of one or morepolypeptides substantially encoded by immunoglobulin genes or fragmentsof immunoglobulin genes. The recognized immunoglobulin genes include thekappa, lambda, alpha, gamma, delta, epsilon and mu constant regiongenes, as well as myriad immunoglobulin variable region genes. Lightchains are classified as either kappa or lambda. Heavy chains areclassified as gamma, mu, alpha, delta, or epsilon, which in turn definethe immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.

A typical immunoglobulin (antibody) structural unit is known to comprisea tetramer. Each tetramer is composed of two identical pairs ofpolypeptide chains, each pair having one “light” (about 25 kD) and one“heavy” chain (about 50-70 kD). The N-terminus of each chain defines avariable region of about 100 to 110 or more amino acids primarilyresponsible for antigen recognition. The terms variable light chain(V_(L)) and variable heavy chain (V_(H)) refer to these light and heavychains respectively.

The term “antibody” as used herein includes antibody fragments thatretain binding specificity. For example, there are a number of wellcharacterized antibody fragments. Thus, for example, pepsin digests anantibody C-terminal to the disulfide linkages in the hinge region toproduce F(ab)′2, a dimer of Fab which itself is a light chain joined toVH-CH1 by a disulfide bond. The F(ab)′2 may be reduced under mildconditions to break the disulfide linkage in the hinge region therebyconverting the (Fab′)2 dimer into an Fab′ monomer. The Fab′ monomer isessentially an Fab with part of the hinge region (see, FundamentalImmunology, W. E. Paul, ed., Raven Press, N.Y. (1993), for a moredetailed description of other antibody fragments). While variousantibody fragments are defined in terms of the digestion of an intactantibody, one of skill will appreciate that fragments can be synthesizedde novo either chemically or by utilizing recombinant DNA methodology.Thus, the term antibody, as used herein also includes antibody fragmentseither produced by the modification of whole antibodies or synthesizedusing recombinant DNA methodologies.

Antibodies include V_(H)-V_(L) dimers, including single chain antibodies(antibodies that exist as a single polypeptide chain), such as singlechain Fv antibodies (sFv or scFv) in which a variable heavy and avariable light region are joined together (directly or through a peptidelinker) to form a continuous polypeptide. The single chain Fv antibodyis a covalently linked V_(H)-V_(L) which may be expressed from a nucleicacid including V_(H)- and V_(L)-encoding sequences either joineddirectly or joined by a peptide-encoding linker (e.g., Huston, et al.Proc. Nat. Acad. Sci. USA, 85:5879-5883, 1988). While the V_(H) andV_(L) are connected to each as a single polypeptide chain, the V_(H) andV_(L) domains associate non-covalently. Alternatively, the antibody canbe another fragment. Other fragments can also be generated, e.g., usingrecombinant techniques, as soluble proteins or as fragments obtainedfrom display methods. Antibodies can also include diantibodies andminiantibodies. Antibodies of the invention also include heavy chaindimers, such as antibodies from camelids.

As used herein, “V-region” refers to an antibody variable region domaincomprising the segments of Framework 1, CDR1, Framework 2, CDR2, andFramework 3, including CDR3 and Framework 4, which segments are added tothe V-segment as a consequence of rearrangement of the heavy chain andlight chain V-region genes during B-cell differentiation. A “V-segment”as used herein refers to the region of the V-region (heavy or lightchain) that is encoded by a V gene. The V-segment of the heavy chainvariable region encodes FR1-CDR1-FR2-CDR2 and FR3. For the purposes ofthis invention, the V-segment of the light chain variable region isdefined as extending though FR3 up to CDR3.

As used herein, the term “J-segment” refers to a subsequence of thevariable region encoded comprising a C-terminal portion of a CDR3 andthe FR4. A germline J-segment is encoded by an immunoglobulin J-genesegment.

As used herein, “complementarity-determining region (CDR)” refers to thethree hypervariable regions in each chain that interrupt the four“framework” regions established by the light and heavy chain variableregions. The CDRs are primarily responsible for binding to an epitope ofan antigen. The CDRs of each chain are typically referred to as CDR1,CDR2, and CDR3, numbered sequentially starting from the N-terminus, andare also typically identified by the chain in which the particular CDRis located. Thus, a V_(H) CDR3 is located in the variable domain of theheavy chain of the antibody in which it is found, whereas a V_(L) CDR1is the CDR1 from the variable domain of the light chain of the antibodyin which it is found.

The sequences of the framework regions of different light or heavychains are relatively conserved within a species. The framework regionof an antibody, that is the combined framework regions of theconstituent light and heavy chains, serves to position and align theCDRs in three dimensional space.

The amino acid sequences of the CDRs and framework regions can bedetermined using various well known definitions in the art, e.g., Kabat,Chothia, international ImMunoGeneTics database (IMGT), and AbM (see,e.g., Johnson et al., supra; Chothia & Lesk, 1987, Canonical structuresfor the hypervariable regions of immunoglobulins. J. Mol. Biol. 196,901-917; Chothia C. et al., 1989, Conformations of immunoglobulinhypervariable regions. Nature 342, 877-883; Chothia C. et al., 1992,structural repertoire of the human VH segments J. Mol. Biol. 227,799-817; Al-Lazikani et al., J. Mol. Biol 1997, 273(4)). Definitions ofantigen combining sites are also described in the following: Ruiz etal., IMGT, the international ImMunoGeneTics database. Nucleic AcidsRes., 28, 219-221 (2000); and Lefranc, M.-P. IMGT, the internationalImMunoGeneTics database. Nucleic Acids Res. January 1; 29(1):207-9(2001); MacCallum et al, Antibody-antigen interactions: Contact analysisand binding site topography, J. Mol. Biol., 262 (5), 732-745 (1996); andMartin et al, Proc. Natl Acad. Sci. USA, 86, 9268-9272 (1989); Martin,et al, Methods Enzymol., 203, 121-153, (1991); Pedersen et al,Immunomethods, 1, 126, (1992); and Rees et al, In Sternberg M. J. E.(ed.), Protein Structure Prediction. Oxford University Press, Oxford,141-172 1996).

“Epitope” or “antigenic determinant” refers to a site on an antigen towhich an antibody binds. Epitopes can be formed both from contiguousamino acids or noncontiguous amino acids juxtaposed by tertiary foldingof a protein. Epitopes formed from contiguous amino acids are typicallyretained on exposure to denaturing solvents whereas epitopes formed bytertiary folding are typically lost on treatment with denaturingsolvents. An epitope typically includes at least 3, and more usually, atleast 5 or 8-10 amino acids in a unique spatial conformation. Methods ofdetermining spatial conformation of epitopes include, for example, x-raycrystallography and 2-dimensional nuclear magnetic resonance. See, e.g.,Epitope Mapping Protocols in Methods in Molecular Biology, Vol. 66,Glenn E. Morris, Ed (1996).

As used herein, “chimeric antibody” refers to an immunoglobulin moleculein which (a) the constant region, or a portion thereof, is altered,replaced or exchanged so that the antigen binding site (variable region)is linked to a constant region of a different or altered class, effectorfunction and/or species, or an entirely different molecule which confersnew properties to the chimeric antibody, e.g., an enzyme, toxin,hormone, growth factor, drug, etc.; or (b) the variable region, or aportion thereof, is altered, replaced or exchanged with a variableregion, or portion thereof, having a different or altered antigenspecificity; or with corresponding sequences from another species orfrom another antibody class or subclass.

As used herein, “humanized antibody” refers to an immunoglobulinmolecule in CDRs from a donor antibody are grafted onto human frameworksequences. Humanized antibodies may also comprise residues of donororigin in the framework sequences. The humanized antibody can alsocomprise at least a portion of a human immunoglobulin constant region.Humanized antibodies may also comprise residues which are found neitherin the recipient antibody nor in the imported CDR or frameworksequences. Humanization can be performed using methods known in the art(e.g., Jones et al., Nature 321:522-525; 1986; Riechmann et al., Nature332:323-327, 1988; Verhoeyen et al., Science 239:1534-1536, 1988);Presta, Curr. Op. Struct. Biol. 2:593-596, 1992; U.S. Pat. No.4,816,567), including techniques such as “superhumanizing” antibodies(Tan et al., J. Immunol. 169: 1119, 2002) and “resurfacing” (e.g.,Staelens et al., Mol. Immunol. 43: 1243, 2006; and Roguska et al., Proc.Natl. Acad. Sci USA 91: 969, 1994).

A “Humaneered™” antibody in the context of this invention refers to anengineered human antibody having a binding specificity of a referenceantibody. A “Humaneered™” antibody for use in this invention has animmunoglobulin molecule that contains minimal sequence derived from adonor immunoglobulin. Typically, an antibody is “Humaneered™” by joininga DNA sequence encoding a binding specificity determinant (BSD) from theCDR3 region of the heavy chain of the reference antibody to human V_(H)segment sequence and a light chain CDR3 BSD from the reference antibodyto a human V_(L) segment sequence. Methods for humaneering are providedin US patent application publication no. 20050255552 and US patentapplication publication no. 20060134098.

The term “binding specificity determinant” or “BSD” as used in thecontext of the current invention refers to the minimum contiguous ornon-contiguous amino acid sequence within a CDR region necessary fordetermining the binding specificity of an antibody. In the currentinvention, the minimum binding specificity determinants reside within aportion or the full-length of the CDR3 sequences of the heavy and lightchains of the antibody.

A “human” antibody as used herein encompasses humanized and Humaneered™antibodies, as well as human monoclonal antibodies that are obtainedusing known techniques.

A “hypofucosylated” antibody preparation refers to an antibodypreparation in which less than 50% of the oligosaccharide chains containα1,6-fucose. Typically, less than about 40%, less than about 30%, lessthan about 20%, less than about 10%, or less than 5% or less than 1% ofthe oligosaccharide chains contain α1,6-fucose in a “hypofucosylated”antibody preparation.

An “afucosylated” antibody lacks α1,6-fucose in the carbohydrateattached to the CH2 domain of the IgG heavy chain.

The term “heterologous” when used with reference to portions of anucleic acid indicates that the nucleic acid comprises two or moresubsequences that are not normally found in the same relationship toeach other in nature. For instance, the nucleic acid is typicallyrecombinantly produced, having two or more sequences, e.g., fromunrelated genes arranged to make a new functional nucleic acid.Similarly, a heterologous protein will often refer to two or moresubsequences that are not found in the same relationship to each otherin nature.

The term “recombinant” when used with reference, e.g., to a cell, ornucleic acid, protein, or vector, indicates that the cell, nucleic acid,protein or vector, has been modified by the introduction of aheterologous nucleic acid or protein or the alteration of a nativenucleic acid or protein, or that the cell is derived from a cell somodified. Thus, e.g., recombinant cells express genes that are not foundwithin the native (non-recombinant) form of the cell or express nativegenes that are otherwise abnormally expressed, under expressed or notexpressed at all. By the term “recombinant nucleic acid” herein is meantnucleic acid, originally formed in vitro, in general, by themanipulation of nucleic acid, e.g., using polymerases and endonucleases,in a form not normally found in nature. In this manner, operably linkageof different sequences is achieved. Thus an isolated nucleic acid, in alinear form, or an expression vector formed in vitro by ligating DNAmolecules that are not normally joined, are both considered recombinantfor the purposes of this invention. It is understood that once arecombinant nucleic acid is made and reintroduced into a host cell ororganism, it will replicate non-recombinantly, i.e., using the in vivocellular machinery of the host cell rather than in vitro manipulations;however, such nucleic acids, once produced recombinantly, althoughsubsequently replicated non-recombinantly, are still consideredrecombinant for the purposes of the invention. Similarly, a “recombinantprotein” is a protein made using recombinant techniques, i.e., throughthe expression of a recombinant nucleic acid as depicted above.

An EphA3-dependent disease, as used herein, refers to a disease in whicha cell that expresses EphA3 is a target for therapy to treat thedisease.

The term “vasculogenic bone marrow precursor cells” refers tobone-marrow-derived endothelial precursors and/or circulatingendothelial cell precursor cells.

The term “cancer cell” or “tumor cell” as used herein refers to aneoplastic cell. The term includes cancer cells that are benign as wellas malignant. Neoplastic transformation is associated with phenotypicchanges of the tumor cell relative to the cell type from which it isderived. The changes can include loss of contact inhibition,morphological changes, and aberrant growth. (see, Freshney, Culture ofAnimal Cells a Manual of Basic Technique (3^(rd) edition, 1994).

“Inhibiting growth of a cancer” in the context of the invention refersto slowing growth and/or reducing the cancer cell burden of a patientthat has cancer “Inhibiting growth of a cancer” thus includes killingcancer cells as well as slowing or arresting cancer cell growth.

As used herein, “therapeutic agent” refers to an agent that whenadministered to a patient suffering from a disease, in a therapeuticallyeffective dose, will cure, or at least partially arrest the symptoms ofthe disease and complications associated with the disease.

The terms “identical” or percent “identity,” in the context of two ormore polypeptide (or nucleic acid) sequences, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues (or nucleotides) that are the same(i.e., about 60% identity, preferably 70%, 75%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specifiedregion, when compared and aligned for maximum correspondence over acomparison window or designated region) as measured using a BLAST orBLAST 2.0 sequence comparison algorithms with default parametersdescribed below, or by manual alignment and visual inspection (see,e.g., NCBI web site). Such sequences are then said to be “substantiallyidentical.” “Substantially identical” sequences also includes sequencesthat have deletions and/or additions, as well as those that havesubstitutions, as well as naturally occurring, e.g., polymorphic orallelic variants, and man-made variants. As described below, thepreferred algorithms can account for gaps and the like. Preferably,protein sequence identity exists over a region that is at least about 25amino acids in length, or more preferably over a region that is 50-100amino acids=in length, or over the length of a protein.

A “comparison window”, as used herein, includes reference to a segmentof one of the number of contiguous positions selected from the groupconsisting typically of from 20 to 600, usually about 50 to about 200,more usually about 100 to about 150 in which a sequence may be comparedto a reference sequence of the same number of contiguous positions afterthe two sequences are optimally aligned. Methods of alignment ofsequences for comparison are well-known in the art. Optimal alignment ofsequences for comparison can be conducted, e.g., by the local homologyalgorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by thehomology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443(1970), by the search for similarity method of Pearson & Lipman, Proc.Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations ofthese algorithms (GAP, BESTFIT, FASTA, and TFASTA in the WisconsinGenetics Software Package, Genetics Computer Group, 575 Science Dr.,Madison, Wis.), or by manual alignment and visual inspection (see, e.g.,Current Protocols in Molecular Biology (Ausubel et al., eds. 1995supplement)).

Preferred examples of algorithms that are suitable for determiningpercent sequence identity and sequence similarity include the BLAST andBLAST 2.0 algorithms, which are described in Altschul et al., Nuc. AcidsRes. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410(1990). BLAST and BLAST 2.0 are used, with the parameters describedherein, to determine percent sequence identity for the nucleic acids andproteins of the invention. The BLASTN program (for nucleotide sequences)uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5,N=−4 and a comparison of both strands. For amino acid sequences, theBLASTP program uses as defaults a wordlength of 3, and expectation (E)of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc.Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation(E) of 10, M=5, N=−4, and a comparison of both strands.

An indication that two polypeptides are substantially identical is thatthe first polypeptide is immunologically cross-reactive with theantibodies raised against the second polypeptide. Thus, a polypeptide istypically substantially identical to a second polypeptide, e.g., wherethe two peptides differ only by conservative substitutions.

The terms “isolated,” “purified,” or “biologically pure” refer tomaterial that is substantially or essentially free from components thatnormally accompany it as found in its native state. Purity andhomogeneity are typically determined using analytical chemistrytechniques such as polyacrylamide gel electrophoresis or highperformance liquid chromatography. A protein that is the predominantspecies present in a preparation is substantially purified. The term“purified” in some embodiments denotes that a protein gives rise toessentially one band in an electrophoretic gel. Preferably, it meansthat the protein is at least 85% pure, more preferably at least 95%pure, and most preferably at least 99% pure.

The terms “polypeptide,” “peptide” and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidue is an artificial chemical mimetic of a corresponding naturallyoccurring amino acid, as well as to naturally occurring amino acidpolymers, those containing modified residues, and non-naturallyoccurring amino acid polymer.

The term “amino acid” refers to naturally occurring and synthetic aminoacids, as well as amino acid analogs and amino acid mimetics thatfunction similarly to the naturally occurring amino acids. Naturallyoccurring amino acids are those encoded by the genetic code, as well asthose amino acids that are later modified, e.g., hydroxyproline,γ-carboxyglutamate, and O-phosphoserine Amino acid analogs refers tocompounds that have the same basic chemical structure as a naturallyoccurring amino acid, e.g., an a carbon that is bound to a hydrogen, acarboxyl group, an amino group, and an R group, e.g., homoserine,norleucine, methionine sulfoxide, methionine methyl sulfonium. Suchanalogs may have modified R groups (e.g., norleucine) or modifiedpeptide backbones, but retain the same basic chemical structure as anaturally occurring amino acid. Amino acid mimetics refers to chemicalcompounds that have a structure that is different from the generalchemical structure of an amino acid, but that functions similarly to anaturally occurring amino acid.

Amino acids may be referred to herein by either their commonly knownthree letter symbols or by the one-letter symbols recommended by theIUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise,may be referred to by their commonly accepted single-letter codes.

“Conservatively modified variants” applies to both amino acid andnucleic acid sequences. With respect to particular nucleic acidsequences, conservatively modified variants refers to those nucleicacids which encode identical or essentially identical amino acidsequences, or where the nucleic acid does not encode an amino acidsequence, to essentially identical or associated, e.g., naturallycontiguous, sequences. Because of the degeneracy of the genetic code, alarge number of functionally identical nucleic acids encode mostproteins. For instance, the codons GCA, GCC, GCG and GCU all encode theamino acid alanine. Thus, at every position where an alanine isspecified by a codon, the codon can be altered to another of thecorresponding codons described without altering the encoded polypeptide.Such nucleic acid variations are “silent variations,” which are onespecies of conservatively modified variations. Every nucleic acidsequence herein which encodes a polypeptide also describes silentvariations of the nucleic acid. One of skill will recognize that incertain contexts each codon in a nucleic acid (except AUG, which isordinarily the only codon for methionine, and TGG, which is ordinarilythe only codon for tryptophan) can be modified to yield a functionallyidentical molecule. Accordingly, often silent variations of a nucleicacid which encodes a polypeptide is implicit in a described sequencewith respect to the expression product, but not with respect to actualprobe sequences.

As to amino acid sequences, one of skill will recognize that individualsubstitutions, deletions or additions to a nucleic acid, peptide,polypeptide, or protein sequence which alters, adds or deletes a singleamino acid or a small percentage of amino acids in the encoded sequenceis a “conservatively modified variant” where the alteration results inthe substitution of an amino acid with a chemically similar amino acid.Conservative substitution tables providing functionally similar aminoacids are well known in the art. Such conservatively modified variantsare in addition to and do not exclude polymorphic variants, interspecieshomologs, and alleles of the invention. Typically conservativesubstitutions for one another: 1) Alanine (A), Glycine (G); 2) Asparticacid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4)Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine(M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7)Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see,e.g., Creighton, Proteins (1984)).

As used in this specification and the appended claims, the singularforms “a,” “an,” and “the” include plural referents unless the contextclearly dictates otherwise.

I. Introduction

The invention relates to antibodies that bind to EphA3 with highaffinity and typically, activate EphA3. The antibodies comprise variableregions with a high degree of amino acid sequence identity to humangerm-line V_(H) and V_(L) sequences. In preferred embodiments, the CDRH3of an antibody of the invention comprises the amino acid sequenceX₁GX₂YEX₃FDX₄ (SEQ ID NO:38), wherein X₁ is S or G, X₂ is Y or V, X₃ isE or D, and X₄ is 5, V, or I, with the proviso that the amino acidsequence is not SGYYEDFDS (SEQ ID NO:39). In some embodimentsembodiment, CDRL3 of an antibody of the invention comprises the aminoacid sequence X₁X₂YX₃X₄YPYT (SEQ ID NO:56), wherein X₁ is G, V or A, X₂is Q, R, or G, X₃ is A, S, or L, and X₄ is N or K.

Typically, the portion of the CDR3 excluding the BSD and the completeFR4 are comprised of human germ-line sequences. In some embodiments, theCDR3-FR4 sequence excluding the BSD differs from human germ-linesequences by not more than 2 amino acids on each chain. In someembodiments, the J-segment comprises a human germline J-segment. Humangermline sequences can be determined, for example, through the publiclyavailable international ImMunoGeneTics database (IMGT) and V-base (onthe worldwide web at vbase.mrc-cpe.cam.ac.uk).

The human germline V-segment repertoire consists of 51 heavy chainV-regions, 40κ light chain V-segments, and 31λ light chain V-segments,making a total of 3,621 germline V-region pairs. In addition, there arestable allelic variants for most of these V-segments, but thecontribution of these variants to the structural diversity of thegermline repertoire is limited. The sequences of all human germ-lineV-segment genes are known and can be accessed in the V-base database,provided by the MRC Centre for Protein Engineering, Cambridge, UnitedKingdom (see, also Chothia et al., 1992, J Mol Biol 227:776-798;Tomlinson et al., 1995, EMBO J 14:4628-4638; and Williams et al., 1996,J Mol Biol 264:220-232).

Antibodies or antibodies fragments as described herein can be expressedin prokaryotic or eukaryotic microbial systems or in the cells of highereukaryotes such as mammalian cells.

An antibody that is employed in the invention can be in any format. Forexample, in some embodiments, the antibody can be an including anconstant region, e.g., a human constant region, e.g., an intact Ig, aFab, Fab′, F(ab′)₂ or a fragment of an intact immunoglobulin, e.g., anscFv or Fv.

II. Heavy Chains

A heavy chain of an anti-EphA3 antibody of the invention comprises aheavy-chain V-region that comprises the following elements:

1) human heavy-chain V-segment sequences comprisingFR1-CDR1-FR2-CDR2-FR3

2) a CDRH3 region comprising the amino acid sequence X₁GX₂YEX₃FDX₄ (SEQID NO:38), wherein X₁ is S or G, X₂ is Y or V, X₃ is E or D, and X₄ is5, V, or I, with the proviso that the amino acid sequence is notSGYYEDFDS (SEQ ID NO:39); and

3) a FR4 contributed by a human germ-line J-gene segment.

In some embodiment, the CDR3 comprises GGYYEDFDS (SEQ ID NO:43),SGYYEEFDS (SEQ ID NO:41), SGVYEDFDS (SEQ ID NO:44), SGYYEDFDV (SEQ IDNO:45), or SGYYEDFDI (SEQ ID NO:46).

The V-segment typically has at least 80% identity, or 85%, 90%, 95%, orgreater identity to a human germline V-segment, e.g., a human VH1subclass. Thus, in some embodiments, the V-segment is a human V_(H)11-02 segment that at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% orgreater, identity to the germ-line segment VH1 1-02. In someembodiments, the V-segment differs by not more than 15 residues from VH11-02 and preferably not more than 10 residues.

In some embodiments, an antibody of the invention comprises a V-segmentthat has at least 90% identity, or at least 91%, 92% 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100% identity to the germ-line segment VH 1-02; or toone of the V-segments of the V_(H) regions shown in FIG. 1.

The FR4 sequence of the antibodies of the invention is provided by ahuman JH1, JH3, JH4, JH5 or JH6 gene germline segment, or a sequencethat has a high degree of amino-acid sequence identity, e.g., at least90% or 95% identity, or differs at not more than 3, typically at notmore than 2 amino acid residues in comparison to a human germline JHsegment. In some embodiments, the J segment is from a human germline JH6sequence and the FR4 has the sequence WGQGTTVTVSS (SEQ ID NO:47).

In some embodiments, the V-segment of the V_(H) region has a CDR1 and/orCDR2 as shown in FIG. 1. For example, an antibody of the invention mayhave a CDR1 that has the sequence GYWMN (SEQ ID NO:48), TYWIS (SEQ IDNO:42), or SYWIN (SEQ ID NO:40). An antibody of the invention may have aCDR2 that has the sequence DIYPGSGNTNYDEKFQG (SEQ ID NO:49),DIYPGSGNTNYAQKFQG (SEQ ID NO:50), DIYPGSGNTNYAQEFRG (SEQ ID NO:51),DIYPGSGNTNYAQKFLG (SEQ ID NO:52), or DIYPGSGNTNYDEKFKR (SEQ ID NO:54).Thus, in some embodiments, an anti-EphA3 antibody of the invention mayhave a V_(H) region CDR3 that has the sequence GGYYEDFDS (SEQ ID NO:43),SGYYEEFDS (SEQ ID NO:41), SGVYEDFDS (SEQ ID NO:44), SGYYEDFDV (SEQ IDNO:45), or SGYYEDFDI (SEQ ID NO:46), and a CDR1 sequence GYWMN (SEQ IDNO:48), TYWIS (SEQ ID NO:42), or SYWIN (SEQ ID NO:40) and a CDR2DIYPGSGNTNYDEKFQG (SEQ ID NO:49), DIYPGSGNTNYAQKFQG (SEQ ID NO:50),DIYPGSGNTNYAQEFRG (SEQ ID NO:51), DIYPGSGNTNYAQKFLG (SEQ ID NO:52), orDIYPGSGNTNYDEKFKR (SEQ ID NO:54).

In some embodiments, an anti-EphA3 antibody of the invention may have aV_(H) region CDR3 that has the sequence SGYYEDFDS (SEQ ID NO:39) and aCDR1 and/or a CDR2 of a VH region set forth in FIG. 1.

In some embodiments, a V_(H) region V-segment of an antibody of theinvention has a V-segment sequence shown in FIG. 1.

In typical embodiment, an antibody of the invention has a V_(H) regionsequence set forth in FIG. 1.

III. Light Chains

A light chain of an anti-EphA3 antibody of the invention comprises atlight-chain V-region that comprises the following elements:

1) human light-chain V-segment sequences comprisingFR1-CDR1-FR2-CDR2-FR3

2) a CDRL3 region that has the sequence CDR3 that comprises the sequenceX₁X₂YX₃X₄YPYT (SEQ ID NO:56), wherein X₁ is G, V or A; X₂ is Q, R, or G;X₃ is A, S, or L; and X₄ is N or K; and

3) a FR4 contributed by a human germ-line J-gene segment.

In some embodiments, the CDR3 has a sequence X₁X₂YX₃X₄YPYT (SEQ IDNO:61), wherein X₁ is V, X₂ is Q, X₃ is A, and X₄ is N. In someembodiments the V_(L) CDR3 is GQYANYPYT (SEQ ID NO:57), VQYAKYPYT (SEQID NO:58), AQYANYPYT (SEQ ID NO:59), VQYSNYPYT (SEQ ID NO:60), VQYANYPYT(SEQ ID NO:61), VGYANYPYT (SEQ ID NO:62), VRYANYPYT (SEQ ID NO:63), orVQYLNYPYT (SEQ ID NO:64).

The V_(L) region comprises either a Vlambda or a Vkappa V-segment. Anexample of a Vkappa sequence that supports binding in combination with acomplementary V_(H)-region is provided in FIG. 1.

The Vkappa segments may be of any subclass, e.g. and is often of the VκIsub-class. In some embodiments, the segments have at least 80% sequenceidentity to a human germline VκI e.g., at least 80% identity to thehuman germ-line VκI L15 sequence. In some embodiments, the Vκ segmentmay differ by not more than 5 residues from VκI L15 In otherembodiments, the V_(L) region V-segment of an antibody of the inventionhas at least 85% identity, or at least 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100% identity to the human kappa V-segmentsequence of a V_(L) region shown in FIG. 1.

The FR4 sequence of the V_(L) region of an antibody of the invention isprovided by a human germline J segment, e.g. or a sequence that has ahigh degree of amino-acid sequence identity to a human germline Jsegment. In some embodiments, the J segment is a human germline Jκ2sequence and the FR4 of the antibody has the sequence FGQGTKLEIK (SEQ IDNO:69).

In some embodiments, the V-segment of the V_(L) region has a CDR1 and/orCDR2 as shown in FIG. 1. Thus, an antibody of the invention may have aCDR1 sequence of RASQGIISYLA (SEQ ID NO:66), QASQDISTYLN (SEQ ID NO:70),RASQEISGYLG (SEQ ID NO:65), or RASQSISSYLA (SEQ ID NO:71) and/or a CDR2sequence AASSLQS (SEQ ID NO:68), GASSLQS (SEQ ID NO:72), AASSLQR (SEQ IDNO:73), or AASTLDS (SEQ ID NO:67).

In particular embodiments, an anti-EphA3 antibody of the invention mayhave a V_(L) region CDR1 and a CDR2 in a combination as shown in one ofthe V-segments of the V_(L) regions set forth in FIG. 1 and a V_(L)region CDR3 sequence that comprises GQYANYPYT (SEQ ID NO:57), VQYAKYPYT(SEQ ID NO:58), AQYANYPYT (SEQ ID NO:59), VQYSNYPYT (SEQ ID NO:60),VQYANYPYT (SEQ ID NO:61), VGYANYPYT (SEQ ID NO:62), VRYANYPYT (SEQ IDNO:63), or VQYLNYPYT (SEQ ID NO:64). In some embodiments, such ananti-EphA3 antibody may comprise a V_(L) region FR4 region that isFGQGTKLEIK (SEQ ID NO:69). Thus, a V_(L) region of an anti-EphA3antibody of the invention, can comprise, e.g., a CDR3 GQYANYPYT (SEQ IDNO:57), VQYAKYPYT (SEQ ID NO:58), AQYANYPYT (SEQ ID NO:59), VQYSNYPYT(SEQ ID NO:60), VQYANYPYT (SEQ ID NO:61), VGYANYPYT (SEQ ID NO:62),VRYANYPYT (SEQ ID NO:63), or VQYLNYPYT (SEQ ID NO:64); a CDR1 sequenceRASQGIISYLA (SEQ ID NO:66), QASQDISTYLN (SEQ ID NO:70), RASQEISGYLG (SEQID NO:65), or RASQSISSYLA (SEQ ID NO:71); and a CDR2 sequence AASSLQS(SEQ ID NO:68), GASSLQS (SEQ ID NO:72), AASSLQR (SEQ ID NO:73), orAASTLDS (SEQ ID NO:67).

In some embodiments, a V_(L) region V-segment of an antibody of theinvention has a V-segment sequence shown in FIG. 1.

In typical embodiment, an antibody of the invention has a V_(L) regionsequence set forth in FIG. 1.

In some embodiments, an antibody of the invention comprises any one ofthe V_(L) regions set forth in SEQ ID NOs:11-23 with any one of theV_(H) regions set forth in SEQ ID NOs: 1-10.

IV. Preparation of EphA3 Antibodies

The affinity of an antibody may be assessed using well known assays todetermine binding activity and affinity. Such techniques include ELISAassays as well as binding determinations that employ surface plasmonresonance or interferometry. For example, affinities can be determinedby biolayer interferometry using a ForteBio (Mountain View, Calif.)Octet biosensor.

Antibodies of the invention typically compete with mIIIA4 for binding toEphA3. The ability of an antibody described herein to block or competewith mIIIA4 for binding to EphA3 indicates that the antibody binds tothe same epitope or to an epitope that is close to, e.g., overlapping,with the epitope that is bound by mIIIA4 for binding to EphA3. In otherembodiments an antibody described herein, e.g., an antibody comprising aV_(H) and V_(L) region combination as shown in the table provided inFIG. 1, can be used as a reference antibody for assessing whetheranother antibody competes for binding to EphA3. A test antibody isconsidered to competitively inhibit binding of a reference antibody, ifbinding of the reference antibody to the antigen is reduced by at least30%, usually at least about 40%, 50%, 60% or 75%, and often by at leastabout 90%, in the presence of the test antibody. Many assays can beemployed to assess binding, including ELISA, as well as other assays,such as immunoblots.

In typical embodiments, the antibody is an activating antibody. Anantibody may be tested to confirm that the antibody retains the activityof activating EphA3. The activity can be determined using any number ofendpoints, including phosphorylation assays, or an indirect endpointsuch as apopotosis.

Methods for the isolation of antibodies with V-region sequences close tohuman germ-line sequences have previously been described (US patentapplication publication nos. 20050255552 and 20060134098). Antibodylibraries may be expressed in a suitable host cell including mammaliancells, yeast cells or prokaryotic cells. For expression in some cellsystems, a signal peptide can be introduced at the N-terminus to directsecretion to the extracellular medium. Antibodies may be secreted frombacterial cells such as E. coli with or without a signal peptide.Methods for signal-less secretion of antibody fragments from E. coli aredescribed in US patent application 20070020685.

To generate a EphA3-binding antibody, one of the V_(H)-regions of theinvention, e.g., shown in FIG. 1, is combined with one of theV_(L)-regions of the invention, e.g., shown in FIG. 1, and expressed inany of a number of formats in a suitable expression system. Thus theantibody may be expressed as a scFv, Fab, Fab′ (containing animmunoglobulin hinge sequence), F(ab′)₂, (formed by di-sulfide bondformation between the hinge sequences of two Fab′ molecules), wholeimmunoglobulin or truncated immunoglobulin or as a fusion protein in aprokaryotic or eukaryotic host cell, either inside the host cell or bysecretion. A methionine residue may optionally be present at theN-terminus, for example, in polypeptides produced in signal-lessexpression systems. Each of the V_(H)-regions described herein may bepaired with each of the V_(L) regions to generate an anti-EphA3antibody.

Antibodies may be produced using any number of expression systems,including both prokaryotic and eukaryotic expression systems. In someembodiments, the expression system is a mammalian cell expression, suchas a CHO cell expression system. Many such systems are widely availablefrom commercial suppliers. In embodiments in which an antibody comprisesboth a V_(H) and V_(L) region, the V_(H) and V_(L) regions may beexpressed using a single vector, e.g., in a discistronic expressionunit, or under the control of different promoters. In other embodiments,the V_(H) and V_(L) region may be expressed using separate vectors. AV_(H) or V_(L) region as described herein may optionally comprise amethionine at the N-terminus.

An antibody of the invention may be produced in any number of formats,including as a Fab, a Fab′, a F(ab′)₂, a scFv, or a dAB. An antibody ofthe invention can also include a human constant region. The constantregion of the light chain may be a human kappa or lambda constantregion. The heavy chain constant region is often a gamma chain constantregion, for example, a gamma-1, gamma-2, gamma-3, or gamma-4 constantregion. In other embodiments, the antibody may be an IgA or IgM.

In some embodiments of the invention, the antibody V_(L) region, e.g., aV_(L) region set forth in FIG. 1, is combined with a human kappaconstant region (e.g., SEQ ID NO:25) to form the complete light-chain.

In some embodiments of the invention, the V_(H) region is combined ahuman gamma-1 constant region. Any suitable gamma-1 allotype can bechosen. Thus, in some embodiments, the antibody is an IgG having aconstant region, e.g., SEQ ID NO:24, that has a V_(H) selected from aV_(H) region sequence set forth in FIG. 1. In some embodiments, theantibody has a V_(L) selected from the V_(L) region sequences set forthin FIG. 1. In particular embodiments, the antibody has a kappa constantregion as set forth in SEQ ID NO:25, and a heavy chain constant regionas set forth in SEQ ID NO:24, where the heavy and light chain variableregions comprise one of the following combinations from the sequencesset forth in FIG. 1.

In some embodiments, e.g., where the antibody is a fragment, theantibody can be conjugated to another molecule, e.g., polyethyleneglycol (PEGylation) or serum albumin, to provide an extended half-lifein vivo. Examples of PEGylation of antibody fragments are provided inKnight et al. Platelets 15:409, 2004 (for abciximab); Pedley et al., Br.J. Cancer 70:1126, 1994 (for an anti-CEA antibody); Chapman et al.,Nature Biotech. 17:780, 1999; and Humphreys, et al., Protein Eng. Des.20: 227, 2007).

In some embodiments, the antibodies of the invention are in the form ofa Fab′ or a (Fab′)₂.

A full-length light chain is generated by fusion of a V_(L)-region tohuman kappa or lambda constant region. Either constant region may beused for any light chain; however, in typical embodiments, a kappaconstant region is used in combination with a Vkappa variable region anda lambda constant region is used with a Vlambda variable region.

The heavy chain of the Fab′ is a Fd′ fragment generated by fusion of aV_(H)-region of the invention to human heavy chain constant regionsequences, the first constant (CH1) domain and hinge region. The heavychain constant region sequences can be from any of the immunoglobulinclasses, but is often from an IgG, and may be from an IgG1, IgG2, IgG3or IgG4. The Fab′ antibodies of the invention may also be hybridsequences, e.g., a hinge sequence may be from one immunoglobulinsub-class and the CH1 domain may be from a different sub-class.

An antibody that is employed in the invention can be in numerousformats. In some embodiments, the antibody can include an Fc region,e.g., a human Fc region. For example, such antibodies include IgGantibodies that bind EphA3 and that have an active isotype. In someembodiments, the antibody can be an active fragment (e.g., it candimerize EphA3) or derivative of an antibody such as an Fab, Fab′,F(ab′)₂, Fv, scFv, or a single domain antibody (“dAb”). For example, insome embodiments, the antibody may be a F(ab′)₂. Other exemplaryembodiments of antibodies that can be employed in the invention includeactivating nanobodies or activating camellid antibodies. Such antibodiesmay additionally be recombinantly engineered by methods well known topersons of skill in the art. As noted above, such antibodies can beproduced using known techniques. As appreciated by one of skill in theart, in some embodiments when an antibody is in a format that can bemonovalent, e.g., an Fv or Fab format, the antibody may be employed as amultivalent antibody, such as a trivalent or tetravalent antibody.Methods of generating multivalent antibodies re known (see, e.g., Kinget al., Cancer Res. 54:6176-6185, 1994).

In many embodiments, an antibody for use in the invention has an Fcconstant region that has an effector function, e.g., binds to an Fcreceptor present on immune effector cells. Exemplary “effectorfunctions” include Clq binding; complement dependent cytotoxicity; Fcreceptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC);phagocytosis; down regulation of cell surface receptors (e.g., B cellreceptor), and the like. Such effector functions generally require theFc region to be combined with a binding domain (e.g. an antibodyvariable domain) and can be assessed using known assays (see, e.g., thereferences cited hereinbelow.)

Anti-EphA3 antibodies that have an active isotype and are bound toFc-receptors on effector cells, such as macrophages, monocytes,neutrophils and NK cells, can induce cell death by ADCC.

The Fc region can be from a naturally occurring IgG1, or other activeisotypes, including IgG3, IgM, IgA, and IgE. “Active isotypes” includeantibodies where the Fc region comprises modifications to increasebinding to the Fc receptor or otherwise improve the potency of theantibody. Such an Fc constant region may comprise modifications, such asmutations, changes to the level of glycosylation and the like, thatincrease binding to the Fc receptor. There are many methods of modifyingFc regions that are known in the art. For example, U.S. PatentApplication Publication No. 20060039904 describes variants of Fcreceptors that have enhanced effector function, including modifiedbinding affinity to one or more Fc ligands (e.g., FcγR, Clq).Additionally, such Fc variants have altered antibody-dependentcell-mediated cytotoxicity (ADCC) and/or complement dependentcytotoxicity (CDC) activity. Other Fc variants include those disclosedby Ghetie et al., Nat Biotech. 15:637-40, 1997; Duncan et al, Nature332:563-564, 1988; Lund et al., J. Immunol 147:2657-2662, 1991; Lund etal, Mol Immunol 29:53-59, 1992; Alegre et al, Transplantation57:1537-1543, 1994; Hutchins et al., Proc Natl. Acad Sci USA92:11980-11984, 1995; Jefferis et al, Immunol Lett. 44:111-117, 1995;Lund et al., FASEB J 9:115-119, 1995; Jefferis et al, Immunol Lett54:101-104, 1996; Lund et al, J Immunol 157:4963-4969, 1996; Armour etal., Eur J Immunol 29:2613-2624, 1999; Idusogie et al, J Immunol164:4178-4184, 200; Reddy et al, J Immunol 164:1925-1933, 2000; Xu etal., Cell Immunol 200:16-26, 2000; Idusogie et al, J Immunol166:2571-2575, 2001; Shields et al., J Biol Chem 276:6591-6604, 2001;Jefferis et al, Immunol Lett 82:57-65. 2002; Presta et al., Biochem SocTrans 30:487-490, 2002; Lazar et al., Proc. Natl. Acad. Sci. USA103:4005-4010, 2006; U.S. Pat. Nos. 5,624,821; 5,885,573; 5,677,425;6,165,745; 6,277,375; 5,869,046; 6,121,022; 5,624,821; 5,648,260;6,194,551; 6,737,056; 6,821,505; 6,277,375; 7,335,742; and 7,317,091;and PCT Publications WO 94/2935; WO 99/58572; WO 00/42072; WO 02/060919,and WO 04/029207.

Glycosylation is a form of post-translational modification by whichcarbohydrates (sugars) are enzymatically linked to macromolecules toproduce glycans. In the context of the present invention, carbohydratesare typically attached to antibody Fc region via one or more N-linkages(through a nitrogen of asparagine or arginine side chains); however,O-linkages (via hydroxy oxygen of serine, threonine, tyrosine,hydroxylysine, or hydroxyproline side chains) are also possible.Generally, IgG antibodies have a conserved N-linked glycosylation sitein the CH2 domain at residue Asn297, while some classes and subclassesalso have 0-linked sugars, often in the hinge region, e.g. IgD and IgAof some species. The sugars are typically complex, high-mannose,branched sugars; in the case of N-linkages, the sugar that attachesdirectly to the amino acid sidechain nitrogen is typically N-acetylglucosamine.

In some embodiments, the glycosylation of Fc regions may be modified.For example, a modification may be aglycosylation, for example, byaltering one or more sites of glycosylation within the antibodysequence. Such an approach is described in further detail in U.S. Pat.Nos. 5,714,350 and 6,350,861. An Fc region can also be made that has analtered type of glycosylation, such as a hypofucosylated Fc varianthaving reduced amounts of fucosyl residues, or an afucosylated Fcvariant lacking fucosyl residues, or an Fc variant having increasedbisecting GlcNAc structures. Such carbohydrate modifications can beaccomplished by, for example, expressing the antibody in a host cellwith altered glycosylation machinery. Cells with altered glycosylationmachinery, including rat myeloma cells as well as yeast and plants, havebeen described in the art and can be used as host cells in which toexpress recombinant antibodies of the invention to thereby produce anantibody with altered glycosylation.

Umana et al, Nat. Biotechnol 17:176-180, 1999, which describes bisectedGlcNac resulting in 10 times ADCC. Umana notes that such bisectedmolecules result in less fucosylation. Davies, et al., Biotechnol.Bioeng. 74:288-294, 2001 describe CHO cells with inserted enzymeβ1-4-N-acetylglucosaminyltransferase III (GnTIII) (which causes thebisected GlcNac structure) resulting in increased ADCC of anti-CD20antibodies. (Umana) U.S. Pat. No. 6,602,684 describes cells engineeredto produce bisecting GlcNac glycoproteins.

Examples of methods to reduce fucosylation of an antibody preparationare provided in Shields et al, J Biol Chem 277:26733-26740, 2002, whichdescribes CHO cells (Lec13) deficient in fucosylation to produce IgG1and further describes that binding of the fucose-deficient IgG1 to humanFcgammaRIIIA was improved up to 50-fold and increased ADCC. In addition,Shinkawa et al., J Biol Chem 278:3466-3473, 2003; compare IgG producedin YB2/0 and CHO cells. The YB2/0 cells have decreased fucosylation andincreased bisecting GlcNac content. Niwa et al., Clinc. Cancer Res.1-:6248-6255, 2004 compare anti-CD20 antibodies with antibodies made inYB2/0 cells (low fucosylation) and observed enhanced ADCC in the latter.Examples of techniques to produce afucosylated antibodies are provided,for example, in Kanda et al, Glycobiology 17:104-118, 2006. U.S. Pat.No. 6,946,292 (Kanda) describes fucosyltransferase knock-out cells toproduce afucosylated antibodies. U.S. Pat. No. 7,214,775 and WO 00/61739describe antibody preparations in which 100% of the antibodies areafucosylated.

Other techniques to modify glycosyation are also known. See, forexample, U.S. Patent Application Publication Nos. 20070248600;20070178551 (GlycoFi technology methods employing engineered lowereukaryotic cells (yeast) to produce “human” glycosylation structures);20080060092 (Biolex technology methods employing engineered plants toproduce “human” glycosylation structures); 20060253928 (which alsodescribed engineering of plants to produce “human” antibodies.

Additional techniques for reducing fucose include ProBioGen technology(von Horsten et al., Glycobiology, (advance access publication Jul. 23,2010); Potelligent™ technology (Biowa, Inc. Princeton, N.J.); andGlycoMAb™ glycosylation engineering technology (GLYCART biotechnologyAG, Zurich, Switzerland).

The N-linked oligosaccharide content of an antibody can be analyzed bymethods known in the art. The following is an example of such a method:Antibodies are subjected to digestion with the enzyme N-glycosidase F(Roche; TaKaRa). Released carbohydrates are analyzed by matrix assistedlaser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) with positive ion mode (Papac et al., Glycobiol. 8: 445-454, 1998).Monosaccharide composition is then characterized by modifiedhigh-performance anion exchange chromatography (HPAEC) (Shinkawa et al.,J. Biol. Chem. 278: 3466-3473, 2003).

In some embodiments of the invention, the antibody is additionallyengineered to reduce immunogenicity, e.g., so that the antibody issuitable for repeat administration. Methods for generating antibodieswith reduced immunogenicity include humanization and humaneeringprocedures and modification techniques such as de-immunization, in whichan antibody is further engineered, e.g., in one or more frameworkregions, to remove T cell epitopes.

In some embodiments, antibodies are employed in a form that can activateEphA3 present on the surface of EphA3-expressing cells, e.g.,vasculogenic bone marrow precursor cells, or that can kill such cells byADCC. Thus, in some embodiments an antibody is dimeric. In otherembodiments, the antibody may be in a monomeric form that has an activeisotype. In some embodiments the antibody is in a multivalent form,e.g., a trivalent or tetravalent form, that can cross-link EphA3.

V. Administration of Anti-EphA3 Antibodies for the Treatment of Diseasesin which EphA3 is a Target

The invention also provides methods of treating a patient that has adisease in which it is desirable to kill EphA3-expressing cells. In someembodiments, such a disease may be a neoplastic disease. Accordingly, inone aspect, the invention provides a method of treating a neoplasticdisease using an antibody of the invention where the method comprisesadministering an anti-EphA3 antibody of the invention to a patient (thathas a tumor) to inhibit tumor growth. Tumors that can be treated includetumors of the breast, lung, colon, stomach, liver, kidney, ovary,esophagus, and prostate, and the others. A solid tumor treated with anantibody of the invention can therefore be a breast carcinoma, lungcarcinoma, prostate carcinoma, gastric carcinoma, esophageal carcinoma,colorectal carcinoma, liver carcinoma, ovarian carcinoma, vulvalcarcinoma, kidney carcinoma, cervical carcinoma, endometrial carcinoma,choriocarcinoma, head and neck cancer, nasopharyngeal carcinoma,laryngeal carcinoma, hepatoblastoma, Kaposi's sarcoma, melanoma, skincarcinoma, hemangioma, cavernous hemangioma, hemangioblastoma,pancreatic carcinoma, retinoblastoma, astrocytoma, glioblastoma,Schwannoma, oligodendroglioma, medulloblastoma, neuroblastomas, sarcomasinclude fibrosarcomas, rhabdomyosarcoma, osteogenic sarcoma,leiomyosarcoma, urinary tract carcinoma, thyroid carcinoma, and Wilm'stumor. Abnormal vascular proliferation associated with phakomatoses, andedema (such as that associated with brain tumors) can also be treatedwith an antibody of the invention.

In some embodiments, the anti-EphA3 antibody is administered to apatient that expresses EphA3 on the surface of the tumor cells. In someembodiments, the anti-EphA3 is administered to a patient that expressesEphA3 on the endothelium of blood vessels in the tumor. In someembodiments, the patient may express EphA3 on both the tumor cellsurface and the endothelium. In some embodiments, the antibody is in aformat as described, e.g., in WO/2008/112192.

In some embodiments, a non-neoplastic condition is treated using anantibody of the invention. The non-neoplastic condition is selected fromthe group consisting of undesired or aberrant hypertrophy, arthritis,rheumatoid arthritis (RA), psoriasis, psoriatic plaques, sarcoidosis,atherosclerosis, atherosclerotic plaques, edema from myocardialinfarction, diabetic and other proliferative retinopathies, retrolentalfibroplasia, neovascular glaucoma, age-related macular degeneration,diabetic macular edema, corneal neovascularization, corneal graftneovascularization, corneal graft rejection, retinal/choroidalneovascularization, neovascularization of the angle (rubeosis), ocularneovascular disease, vascular restenosis, arteriovenous malformations(AVM), meningioma, hemangioma, angiofibroma, thyroid hyperplasias(including Grave's disease), corneal and other tissue transplantation,chronic inflammation, lung inflammation, acute lung injury/ARDS, sepsis,primary pulmonary hypertension, malignant pulmonary effusions, cerebraledema (e.g., associated with acute stroke/closed head injury/trauma),synovial inflammation, pannus formation in RA, myositis ossificans,hypertropic bone formation, osteoarthritis (OA), refractory ascites,polycystic ovarian disease, endometriosis, 3rd spacing of fluid diseases(pancreatitis, compartment syndrome, burns, bowel disease), uterinefibroids, premature labor, chronic inflammation such as IBD (Crohn'sdisease and ulcerative colitis), renal allograft rejection, inflammatorybowel disease, nephrotic syndrome, undesired or aberrant tissue massgrowth (non-cancer), obesity, adipose tissue mass growth, hemophilicjoints, hypertrophic scars, inhibition of hair growth, Osier-Webersyndrome, pyogenic granuloma retrolental fibroplasias, scleroderma,trachoma, vascular adhesions, synovitis, dermatitis, preeclampsia,ascites, pericardial effusion, and pleural effusion.

In some embodiments, an antibody of the invention is administered to apatient suffering from a myeloproliferative disorder. In someembodiments, the myeloproliferative disorder is acute myeloid leukemia,chronic myeloid leukemia, myelodysplastic syndrome, polycythemia vera(PV), essential thrombocythemia (ET), or idiopathic myelofibrosis (IM).In some embodiments, an anti-EphA3 antibody of the invention can be usedin combination with one or more additional therapeutic agents to treat apatient that has chronic myeloid leukemia where leukemic stem cells fromthe patient express EphA3. Such therapeutic agents include variouschemotherapeutic agents and imatinib mesylate (GLEEVEC®).

The antibody may be administered alone, or in combination with othertherapies to treat the disease of interest. In some embodiments, theanti-EphA3 antibody is administered in combination with a Bv8antagonist, e.g., a Bv8 antibody antagonist. Bv8 antagonists are known(see, e.g., WO 2009039337 and the references relating to Bv8 antagonistscited therein). For example, Bv8 antagonists include, antibodies andantibody fragments specifically binding to a native sequence Bv8polypeptide, or a native sequence Bv8 receptor (PKR-I/EG-VEGFR1 orPKR-2/EG-VEGFR2) polypeptide. In some embodiments, a patient may also betreated with additional therapeutic agents, including a VEGF antagonist,e.g., an anti-VEGF antibody antagonist, as well as other therapeuticagents, examples of which are additionally described below.

In some embodiments, the anti-EphA3 antibody is administered to apatient that has previously been treated with a VEGF antagonist, e.g.,an anti-VEGF antibody antagonist. In some embodiments, the tumor may berefractory to treatment with a VEGF antagonist. In some embodiments, theanti-EphA3 antibody is administered to a patient that has an early stagetumor, e.g., a Stage I, Stage II, or Stage III tumor.

A patient that is considered to be refractory to treatment with a VEGFantagonist, e.g., a VEGF antibody antagonist, or has a tumor that isrefractory to treatment with a VEGF antagonist as used herein refers toa patient who responds to therapy, but suffer from side effects,develops resistance, does not respond to the therapy, does not respondsatisfactorily to the therapy, etc. Thus, in such patients, or thetumors from such patients, the number of tumor cells has not beensignificantly reduced, or has increased, or tumor size has not beensignificantly reduced, or has increased, or there is not furtherreduction in size or in number of cancer cells. The determination thatthe patient is refractory to treatment can be made either in vivo or invitro by any method known in the art for assaying the effectiveness oftreatment on cancer cells. Similarly, a patient who has a non-neoplasticcondition that is refractory to treatment with a VEGF antagonist, e.g.,a VEGF antibody, in the context of this invention refers to a patientwho does not respond satisfactorily to treatment with the VEGFantagonist, for example, the patient suffers side effects, developsresistance, or does not exhibit reduction in therapeutic indicators forthe condition.

The methods of the invention comprise administering an anti-EphA3antibody as a pharmaceutical composition to a patient in atherapeutically effective amount using a dosing regimen suitable fortreatment of the disease. The composition can be formulated for use in avariety of drug delivery systems. One or more physiologically acceptableexcipients or carriers can also be included in the compositions forproper formulation. Suitable formulations for use in the presentinvention are found in Remington: The Science and Practice of Pharmacy,21st Edition, Philadelphia, Pa. Lippincott Williams & Wilkins, 2005.

The anti-EphA3 antibody is provided in a solution suitable for injectioninto the patient such as a sterile isotonic aqueous solution forinjection. The antibody is dissolved or suspended at a suitableconcentration in an acceptable carrier. In some embodiments the carrieris aqueous, e.g., water, saline, phosphate buffered saline, and thelike. The compositions may contain auxiliary pharmaceutical substancesas required to approximate physiological conditions, such as pHadjusting and buffering agents, tonicity adjusting agents, and the like.

The pharmaceutical compositions of the invention are administered to apatient, e.g., a patient that has a tumor or non-neoplastic condition,in an amount sufficient to cure or at least partially arrest the diseaseor symptoms of the disease and its complications. An amount adequate toaccomplish this is defined as a “therapeutically effective dose.” Atherapeutically effective dose is determined by monitoring a patient'sresponse to therapy. Typical benchmarks indicative of a therapeuticallyeffective dose include amelioration of symptoms of the disease in thepatient. Amounts effective for this use will depend upon the severity ofthe disease and the general state of the patient's health, includingother factors such as age, weight, gender, administration route, etc.Single or multiple administrations of the antibody may be administereddepending on the dosage and frequency as required and tolerated by thepatient. In any event, the methods provide a sufficient quantity ofanti-EphA3 antibody to effectively treat the patient.

The antibody can be administered by injection or infusion through anysuitable route including but not limited to intravenous, sub-cutaneous,intramuscular or intraperitoneal routes. In some embodiments, theantibody may be administered by insufflation. In an exemplaryembodiment, the antibody may be stored at 10 mg/ml in sterile isotonicaqueous saline solution for injection at 4° C. and is diluted in either100 ml or 200 ml 0.9% sodium chloride for injection prior toadministration to the patient. The antibody is administered byintravenous infusion over the course of 1 hour at a dose of between 0.2and 10 mg/kg. In other embodiments, the antibody is administered byintravenous infusion over a period of between 15 minutes and 2 hours. Instill other embodiments, the administration procedure is viasub-cutaneous bolus injection.

The dose of antibody is chosen in order to provide effective therapy forthe patient and is in the range of less than 0.1 mg/kg body weight toabout 25 mg/kg body weight or in the range 1 mg-2 g per patient.Preferably the dose is in the range 1-10 mg/kg or approximately 50mg-1000 mg/patient. The dose may be repeated at an appropriate frequencywhich may be in the range once per day to once every three months,depending on the pharmacokinetics of the antibody (e.g., half-life ofthe antibody in the circulation) and the pharmacodynamic response (e.g.,the duration of the therapeutic effect of the antibody). In someembodiments, the in vivo half-life of between about 7 and about 25 daysand antibody dosing is repeated between once per week and once every 3months. In other embodiments, the antibody is administered approximatelyonce per month.

A V_(H) region and/or V_(L) region of the invention may also be used fordiagnostic purposes. For example, the V_(H) and/or V_(L) region may beused for clinical analysis, such as detection of EphA3 levels on cellsfrom a patient. A V_(H) or V_(L) region of the invention may also beused, e.g., to produce anti-Id antibodies.

EXAMPLES Methodology Sub-Cloning of Murine V-regions

The V-region DNA from murine monoclonal mIIIA4 were provided by Dr.Martin Lackmann (Department of Biochemistry and Molecular Biology,Monash University, Victoria, Australia). PCR was used to amplify theV-genes of the V-heavy and V-kappa regions and incorporate restrictionenzyme sites suitable for cloning into the desired vectors. V-regionswere cloned as Fab fragments and expressed in E. coli. This Fab wastested for EphA3-Fc antigen binding and is referred to as referencesequence FA4 in these examples.

Antibody Purification

Fab fragments were expressed by secretion from E. coli. Cells were grownin 2×YT medium to an OD₆₀₀ of 0.6. Expression was induced using IPTG for3 hours at 33° C. Assembled Fabs were obtained from periplasmicfractions and purified by affinity chromatography using StreptococcalProtein G (HiTrap Protein G HP columns; GE Healthcare) according tostandard methods. Fabs were eluted in pH 2.0 buffer, immediatelyadjusted to pH 7.0 and dialyzed against PBS pH 7.4 (PBS is withoutcalcium and magnesium).

ELISA

Typically 50 ng of antigen was bound to a 96 well microtiter plate byovernight incubation at 4° C. The plate was blocked with a solution of5% milk in PBS for one hour at 33° C. Induced medium (50 μl) from E.coli expressing each Humaneered Fab or optimized reference Fab FA106 wasadded to each well. After a one hour incubation at 33° C., the plate wasrinsed three times with PBS+0.1% Tween 20 (PBST), 50 μl ofanti-human-kappa chain HRP conjugate (Sigma; diluted to 0.1 ng/ml inPBST) was added to each well, and the plate was incubated for 40 min at33° C. The plate was washed three times with PBST and once with PBS. Thesubstrate 3,3′,5,5′ tetramethylbenzidine (TMB), 100 μl (Sigma), wasadded to each well and the plate was incubated for ˜5 min at roomtemperature. To stop the reaction, 100 μl of 0.2 N H₂SO₄ was added toeach well. The reactions were read at 450 nm by spectrophotometry.

For detection of binding to Eph family members, recombinant human Ephextracellular (ec) domains were obtained from R&D Systems Inc: EphA1-Fcfusion protein, EphA2 ec domain, EphA5 ec domain, EphB4 ec domain andEphB6-Fc fusion protein. ELISA wells were coated with 100 ng of Ephprotein for 1 hr at 37° C. After washing once with PBST, wells wereblocked with 5% milk in PBST at 37° C. for one hour. Wells were washedonce and a two fold dilution series of candidate humaneered antibodyadded to each set of coated Eph proteins. After one hour, the wells werewashed three times in PBST and 50 μl of anti-human-kappa chain HRPconjugate (Sigma; diluted to 0.1 ng/ml in PBST) was added to each well.The plate was incubated for 45 minutes, washed 3 times with PBST, washedone with PBS and 100 μl of TMB added to each well. The reaction wasstopped by addition of 0.2N H₂SO₄ and binding measured by absorbance at450 nm.

Colony Lift Binding Assay (CLBA)

Screening of Humaneered libraries of Fab fragments was carried out asdescribed (U.S patent Application Publication Nos. 20050255552 and20060134098) using antigen coated nitrocellulose filters.

Affinity Measurements

The binding kinetics of Fab fragments were analyzed using surfaceplasmon resonance analysis (spr; Biacore T100) at Biosensor Tools Inc.Affinities were calculated from the determined association anddissociation constants at three different Fab concentrations.

Construction of IgGs

Chimeric IIIA4 IgG was constructed to contain human IgG1 constantregions and variable regions from the original mouse IIIA4 antibody. PCRwas used to amplify the heavy and light chains from mouse IIIA4 DNAprovided by Martin Lackmann and also to incorporate restriction sitesfor cloning. The heavy chain variable region was cloned into a vectorexpressing the full IgG1 heavy chain expressed from a CMV promoterlocated downstream of a UCOE sequence. The plasmid contains the Neo genefor selection in mammalian cells and the Amp gene for plasmid productionin E. coli. Similarly, the light chain variable region was cloned into avector expressing the human kappa light chain constant region, expressedfrom a CMV promoter downstream of a UCOE sequence. The plasmid containsa gene for hygromycin selection in mammalian cells and the Amp gene forproduction in E. coli. Engineered antibody IgG heavy and light chainvectors were constructed similarly except the DNA for the variableregions was obtained from E. coli expression vectors described above andthe heavy chain expression vector contained the puromycin resistancegene instead of neomycin. Humaneered antibody IgG and chimeric IIIA4 IgGwere expressed in a modified CHO cell line by cotransfection of theheavy and light chain constructs using Fugene 6 reagent (Promega).

Flow Cytometry

Typically, 3×10⁶ cells of SKme128, LnCAP and B16-F10 were collected bycentrifugation at 3000 rpm for 3 minutes. Media were removed and thecells blocked with 2% BSA in PBS for 30 minutes at 4° C. followed by asecond block with 10 μg/ml rat IgG for 30 minutes at 4° C. Cells werepelleted, re-suspended in 1.5 ml PBS and divided into 500 μl aliquots.Each aliquot was probed separately with 5 μg/ml of control IgG,humaneered IgG or chimeric IIIA4 IgG for 45 minutes at 4° C. The sampleswere washed once in PBS and anti-human IgG-phycoerythrin-conjugate wasadded. After 45 minutes, cells were washed once, re-suspended in PBS andanalyzed by flow cytometry using a FACS Caliber flow cytometery.Propidium iodide was added just prior to analysis to exclude dead cells.

Example 1 Identification of Engineered Human Anti-EphA3 Antibodies

Murine and Reference V-region Amino Acid Sequences Murine (mIIIA4) and areference (FA4) V-region sequences are shown below. CDR sequences areunderlined.

mIIIA4 and FA4 Vh (SEQ ID NO: 78):EVKLEESGAELVKPGSSVKLSCKASGYNFTSYWINWVRLRPGQGLEWIGDIYPGSGNTNYDEKFKRKATLTVDTSSSTAYMQLSSLASEDSALY YCTRSGYYEDFDSWGQGTTLIVSSmIIIA4 and FA4 Vk (SEQ ID NO: 79):DIVLTQTPSSLSASLEERVSLTCRASQEISGYLGWLQQKPDGTIKRLIYAASTLDSGVPKKFSGNRSGSEYSLTISSLESEDFADYYCVQYANY PYTFGGGTKLEIK

The Fab FA4 has intact murine V-regions from mIIIA4 fused with humanconstant regions and was purified from E. coli. A dilution ELISA of Fabfragments binding to the antigen produced binding curves that weredependent on antibody concentration.

In addition to the reference Fab (FA4), an optimized reference Fab(FA106) was constructed. Several framework amino acid residues in FA4were changed to human germ-line in the optimized reference Fab FA106.The V-region sequences of the optimized reference Fab are providedbelow. The residues altered to human germ-line are shown as bold font.CDR sequences are underlined.

FA106 Vh (SEQ ID NO: 80):EVKLEESGAELVKPGSSVKLSCKASGYNFTSYWINWVRLRPGQGLEWIGDIYPGSGNTNYDEKFKRKATLTVDTSSSTAYMQLSSLASEDTAVYYC ARSGYYEDFDSWGQGTTVTVSSFA106 Vk (SEQ ID NO: 81):DIVLTQTPSSLSASLEERVSLTCRASQEISGYLGWLQQKPDGTIKRLIYAASTLDSGVPKKFSGNRSGSEYSLTISSLESEDFATYYCVQYANYPY TFGQGTKLEIK

Library Construction and V-Region Cassettes

Epitope-focused libraries were constructed from a human V-segmentlibrary sequences linked to the unique CDR3-FR4 region containing theBSD and human germ-line J-segment sequences. The “full-length” Vh (Vh1and Vh5) and Vk (VkI) libraries were used as a base for construction of“cassette” libraries in which only part of the murine V-segment isinitially replaced by a library of human sequences. Several types ofcassettes “libraries” were constructed for both the Vh and Vk chains.Cassettes for the V-heavy and V-kappa chains were made by bridge PCRwith overlapping common sequences within the framework 2 region. In thisway “front-end” human cassette libraries were constructed for both humanVh1 and Vh5 subclasses and a “middle” human cassette library wasconstructed for human Vh1. “Front end” and “middle” cassette librarieswere constructed for the Vk I subclass.

Additionally, a cassette library consisting of Vh CDR2-FR3 wasconstructed. A schematic is shown in FIG. 2. The first four residues(boxed) of the reference CDR2 were encoded by the 5′ PCR primer. Also,the underlined amino acid residues in the mIIIA4 CDR2 and the humangerm-line Vh1-58 CDR2 were varied in pair-wise combination in theforward primer (shown by the amino acid residues above and below theline). The 3′ PCR primer is complementary to human germ-line Vh1 FR3.The primers were used to amplify and append a Hu Vh1 FR3 library(derived from spleen mRNA) to the engineered CDR2 library. Consecutivebridge PCR reactions were used to attach “front end” and CDR3-FR4cassettes to construct a functional V-region.

Human Vh or Vk cassettes that supported binding to the antigen wereidentified by colony-lift binding assay and a rank order was determinedaccording to affinity by ELISA. V-heavy screening identified“front-end”, “middle” and CDR2/FR3 cassettes that supported EphA3-Fcrecombinant fusion protein antigen binding. V-kappa screening identified“front-end” and “middle” cassettes that supported antigen binding. Thefunctional cassettes for each chain were recombined to construct a fullyengineered, high affinity Fab that bound antigen.

After the identification of a pool of high affinity, engineered Fabs,CDR3 affinity maturation libraries were built. The common CDR3 BSDsequences of a panel of engineered Fab clones were mutated usingdegenerate PCR primers to generate libraries. These mutagenic librarieswere screened using colony lift binding and ELISA assays. The selectedFabs were ranked for affinity with ELISA. Mutations that supportedsimilar or improved affinity for antigen when compared to the FA106 Fabwere identified. The heavy chain and light chain CDR3 mutations thatsupport or improve antigen binding help to define the BSD region foreach CDR.

Reference and Humaneered Fab Sequence Alignment

Aligned V-segments of murine reference and two engineered Fabs aminoacid sequences were compared with the closest single human germ-lineV-gene, Vh1-02 or VkI L15. The FR4 for the humaneered Fab Vh-regions isfrom human germ-line JH6 and has the sequence WGQGTTVTVSS (SEQ IDNO:47). The FR4 for the humaneered Fab Vk-regions is from humangerm-line Jk2 and has the sequence FGQGTKLEIK (SEQ ID NO:69).

Each of the Vh-regions and Vk-regions of the engineered Fabs have a highhomology to human germ-line amino acid sequence. Exemplary homologiesare shown in Table 1.

TABLE 1 Percentage identity to human germ-line sequence for twoengineered V-regions: all percentages represent identity to a singlehuman germ-line sequence across the V-region and exclude the CDR3 BSDsequences Humaneered Fab Vh versus Vh1-02 Vk versus VkI L15 1 93% 95% 291% 95%

Example 2 Binding Kinetics of Engineered Antibodies

Engineered Fabs were isolated from colony-lift binding assays andaffinity confirmed by antigen-binding ELISA. Engineered Fab clones withstrong positive signals in antigen-binding ELISA were purified andfurther characterized by kinetic comparison with the optimized referenceFab FA106.

Binding kinetics of two engineered Fabs and reference Fab FA106 wereanalyzed using a Biacore. The three Fabs were diluted from the startingconcentration of 500 nM to 100 nM and further tested in a three-folddilution series using PBS, pH 7.4 with 0.005% Tween-20 and 0.1 mg/mlBSA. Each of the five concentrations was tested three times over thethree different density surfaces. Assays were run at 25° C. The responsedata from each surface were fit to a 1:1 interaction model. Calculatedassociation and dissociation constants are shown in Table 2. Kineticanalysis of engineered Fab clones 1 and 2 and the reference clone FA106all showed low nanomolar affinities for the antigen.

TABLE 2 Humaneered Fab Binding constants determined at 25 degrees C.k_(a) (M⁻¹s⁻¹) k_(d) (s⁻¹) K_(D) (nM) Low 1.83E6 0.00193 1.052 medium1.01E6 0.001513 1.5 high 1.60E6 0.00186 1.16 Humaneered Fab 1 avg1.4(4)E6   1.7(2)E−3 1.2(2) low 4.10E6 0.0058 1.4 medium 6.11E5 0.001782.91 high 1.67E6 0.00345 2.06 FA106 avg 2(1)E6   3(2)E−3 2.1(8) low5.14E5 0.00332 6.45 medium 6.50E5 0.00399 6.16 high 3.52E5 0.00279 7.92Humaneered Fab 2 avg 5(1)E5 3.3(6)E−3 6.8(9) The number in parenthesesrepresents the standard error in the last reported digit based on thedata from the three different density surfaces. The terms “low”,“medium”, and “ high” in the left column refer to chip densities.

Humaneered Fab1 was expressed as an IgG in mammalian cells and purifiedfrom culture supernatant. Fab fragment was generated by papain digestionfor analysis of monovalant binding affinity. Binding of Fab to human andmouse EphA3-Fc was measured on a Biacore 3000 using biotinylated EphA3variants captured on a Streptavidin chip. Fab was diluted in HBSPrunning buffer from 50 nM to 0.62nM with 3× dilutions. Results weredouble blanked with an empty reference cell and multiple HBSP bufferinjections. Global fit analysis of the Biacore data was carried outassuming a 1:1 interaction. The binding kinetics parameters are shown inTable 3. The data show that Humaneered Fab1 produced from mammaliancells binds with high affinity to both human and murine EphA3.

TABLE 3 Engineered Fab 1 Binds Human and Mouse EphA3 with ComparableAffinity Analyte k_(a) (1/Ms) k_(d) (1/s) K_(D) (pM) Human EphA3-Fc 2.2× 10⁶ 2.0 × 10⁻³ 930 Mouse EphA3-Fc 2.3 × 10⁶ 1.8 × 10⁻³ 800 Binding ofFab 1 to immobilized mouse and human EphA3-Fc fusion proteins wasanalyzed by surface plasmon resonance analysis using a Biacore 3000instrument and global fit analysis. k_(a) = association constant; k_(d)= dissociation constant; K_(D) = overall affinity.

Binding and Specificity

A full-length antibody (IgG1κ) was constructed, expressed from CHO cellsand purified by Protein A affinity chromatography. ELISA plates werecoated with EphA3-Fc and binding of cIIIA4 IgG, an exemplary engineeredIgG, and a control IgG1 were compared (FIG. 3). The EC₅₀ in this assaywas approximately three-fold lower for the engineered IgG than for theoriginal chimeric antibody.

EphA3 is a member of the Eph receptor family which binds Ephrin ligands.The most homologous members of the family are the EphA receptors whoseextracellular domains vary between 39% and 62% sequence identity toEphA3.

To confirm the specificity of the exemplary engineered IgG, binding wasassessed against three EphA proteins and two more distantly related EphBproteins (see FIG. 4). EphA5 homology to EphA3 is 61% and represents oneof the most homologous family members to EphA3. The engineered antibodybound EphA3 specifically; binding was not observed to EphA1, EphA2 orEphA5. There was also no detectable binding to either of two EphBreceptors tested (EphB4 and EphB6).

The exemplary engineered antibody was also tested for binding to EphA3expressed on the surface of live cells. Three tumor cell lines known toexpress EphA3 were used: a mouse melanoma (B16), a human melanoma(SKme128), and a prostate cancer line (LnCAP). Live cells were probedwith the engineered IgG, chimeric IIIA4 or a control antibody. Boundantibody was detected using flow cytometry by an anti-human IgGphycoerythrin conjugate (FIG. 5). Strong binding was observed for boththe engineered IgG and Chimeric IIIA4 to B16 and SKme128 cells. BothIgGs also bound LnCAP.

Example 3 Evaluation of the Ability of Fab and F(Ab′)2 Fragments toInduce Apoptosis

Fab fragments were generated by papain digestion of an exemplaryengineered IgG1 antibody of the invention (Ab1) or control human IgG1antibody. One mg of antibody was incubated with 0.01 mg of papain (Roche#10108014001) in 100 mM Sodium Acetate pH 5.0 at 37° C. for 18 h.F(ab′)2 was produced by pepsin digestion. Five mg of IgG was incubatedwith 250 μl immobilized pepsin agarose slurry (Pierce #20343) at 37° C.for 18 h in 100 mM Sodium Acetate pH 4.0. Upon cleavage, both digestswere incubated with protein A resin for 30 minutes to remove Fcfragments and the supernatants were collected. Fab and F(ab′)₂ fragmentswere dialyzed into 50 mM Na Succinate pH 6.0, 145 mM NaCl and 0.05%Tween 80.

To evaluate the ability of Fab and F(ab′)₂ fragments of Ab1 to induceapoptosis in primary cells isolated from leukemia patients, cells wereseeded at 2×10⁵ cells/well in 96-well “U”-bottom plates in 0.1 mlculture medium (RPMI 1640 with 10% fetal bovine serum). Antibody orantibody fragment was added to final concentrations of 10 μg/ml and theplates were incubated at 37° C. and 5% carbon dioxide in atissue-culture incubator for 24 hours. As a positive control forapoptosis induction, separate cell samples were incubated withcamptothecin (10 μM; Calbiochem). At the end of the incubation, cellswere harvested and washed by centrifugation at 1000 rpm for 5 minfollowed by incubation in 0.1 ml buffer containing 10 μl FITC-conjugatedAnnexin V (BD Pharmingen) for 30 minutes on ice. Cells were washed onceby centrifugation and resuspended in flow cytometry buffer containingpropidium iodide (Sigma) diluted 1:1000. Annexin V-staining cellsundergoing apoptosis were identified by flow cytometry.

TABLE 4 Induction of apoptosis by Ab1 antibody and antibody fragmentsApoptosis (%) Apoptosis (%) Treatment Experiment 1 Experiment 2Engineered Ab1 IgG 82.0 85 hIgG1 control 1.8 — (Fab′)₂ 16.3 23 (Fab′)₂control 1.3 0.8 Engineered Ab1 Fab 1.1 1.1 Fab control 0 0 Camptothecin91.0 97.0

The results in Table 4 show that an exemplary antibody (Ab1) F(ab′)₂fragment induced direct induction of apoptosis in primary leukemia cellsexpressing EphA3. Approximately 20% of the target cells were killedwithin 24 hours using 10 μg/ml Ab1 F(ab′)₂. In contrast, the monovalentFab fragment was not able to induce detectable levels of apoptosis,indicating that dimerization of EphA3 is necessary and sufficient toinduce significant levels of apoptosis in these cells and Fc effectorfunctions are not required for apoptosis induction.

Example 4 Evaluation of an Afucosylated Antibody

Antibody 1 was produced in two glycosylation forms by expression indifferent CHO cell lines. One form (fucosylated Antibody 1) hasglycosylation patterns typical of an IgG1κ (f-allotype) therapeuticantibody including a 1,6 fucose. The other form (designated afucosylatedAntibody 1) is produced in a CHO cell line containing a homozygousdeletion of the α-1,6 fucosyl transferase gene FUT8 to prevent theaddition of α-1,6 fucose and is therefore afucosylated. These antibodypreparations were compared in NK-cell mediated antibody-dependentcellular cytotoxicity (ADCC) assays.

Different concentrations of anti-EphA3 antibody preparations wereincubated with leukemia primary target cells and normal human PBMCeffector cells (Buffy coat from Stanford University Blood Bank). Bothfucosylated Antibody 1 and afucosylated Antibody 1 at 0.0001 μg/mL to10.0 μg/mL were tested with 1×10⁴ target cells from a patient with acutemyeloid leukemia (AML) and 1×10⁶ normal PBMC effector cells (100:1effector:target cell ratio). After 16 hours incubation at 37° C., 5%CO₂, LDH release was measured in comparison with LDH fromdetergent-lysed cells to determine the percent cytotoxicity (using aPromega Cytotox 96 kit).

Afucosylated Antibody 1 shows increased ADCC activity againstEphA3-positive target cells compared with fucosylated Antibody 1 (FIG.6).

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be readily apparent to one of ordinary skill inthe art in light of the teachings of this invention that certain changesand modifications may be made thereto without departing from the spiritor scope of the appended claims.

All publications, accession numbers, patents, and patent applicationscited in this specification are herein incorporated by reference as ifeach was specifically and individually indicated to be incorporated byreference.

What is claimed is:
 1. An anti-EphA3 antibody, comprising: a V_(H)region that has: a CDR3 comprising the amino acid sequenceX₁GX₂YEX₃FDX₄, (SEQ ID NO:38) wherein X₁ is S or G, X₂ is Y or V, X₃ isE or D, and X₄ is 5, V, or I, with the proviso that when the amino acidsequence is SGYYEDFDS (SEQ ID NO:39), the CDR1 is not SYWIN (SEQ IDNO:40) and when the amino acid sequence is SGYYEEFDS (SEQ ID NO:41), theCDR1 is not TYWIS (SEQ ID NO:42); a J segment that has no more than twoamino acid changes relative to a human germline J segment amino acidsequence; and a V-segment that comprises at least 90% identity to ahuman germ line V-segment amino acid sequence; and a V_(L) region thathas: a CDR3 comprising the sequence X₁X₂YX₃X₄YPYT (SEQ ID NO:56),wherein X₁ is G, V, or A; X₂ is Q, R, or G; X₃ is A, S, or L; and X₄ isN or K; a J segment that comprises at least 90% identity to a humangermline J segment amino acid sequence; and a V-segment that comprisesat least 90% identity to a human germ line V-segment amino acidsequence.
 2. The antibody of claim 1, wherein the J segment has no morethan two amino acid changes relative to a human JH6 amino acid sequence,and the V-segment comprises at least 90% identity to a human VH1 1-02amino acid sequence
 3. The antibody of claim 1, wherein FR4 comprisesWGQGTTVTVSS (SEQ ID NO:47).
 4. The antibody of claim 1, wherein the CDR3comprises GGYYEDFDS (SEQ ID NO:43), SGYYEEFDS (SEQ ID NO:41), SGVYEDFDS(SEQ ID NO:44), SGYYEDFDV (SEQ ID NO:45), or SGYYEDFDI (SEQ ID NO:46).5. The antibody of claim 4, wherein the V_(H) region CDR1 has thesequence GYWMN (SEQ ID NO:48), TYWIS (SEQ ID NO:42), or SYWIN (SEQ IDNO:40) and the V_(H) region CDR2 has the sequence DIYPGSGNTNYDEKFQG (SEQID NO:49), DIYPGSGNTNYAQKFQG (SEQ ID NO:50), DIYPGSGNTNYAQEFRG (SEQ IDNO:51), DIYPGSGNTNYAQKFLG (SEQ ID NO:52), DIYPGSGNTNYDEKFEG (SEQ IDNO:53), or DIYPGSGNTNYDEKFKR (SEQ ID NO:54).
 6. The antibody of claim 1,wherein the V-segment sequence has a V_(H) V-segment sequence shown inFIG.
 1. 7. The antibody of claim 1, wherein the V_(H) has the sequenceof a V_(H) region set forth in FIG.
 1. 8. The antibody of claim 1,wherein the V_(L) region J segment has no more than two amino acidchanges in comparison to human germ-line Jκ2 amino acid sequenceFGQGTKLEIK (SEQ ID NO:69) and the V-segment comprises at least 90%identity to human germline JκI L15 amino acid sequence.
 9. The antibodyof claim 1, wherein the V_(L) FR4 comprises the amino acid sequenceFGQGTKLEIK (SEQ ID NO:69).
 10. The antibody of claim 1, wherein theV_(L) region CDR3 comprises GQYANYPYT (SEQ ID NO:57), VQYAKYPYT (SEQ IDNO:58), AQYANYPYT (SEQ ID NO:59), VQYSNYPYT (SEQ ID NO:60), VQYANYPYT(SEQ ID NO:61), VGYANYPYT (SEQ ID NO:62), VRYANYPYT (SEQ ID NO:63), orVQYLNYPYT (SEQ ID NO:64).
 11. The antibody of claim 10, wherein theV_(L) region CDR1 has the sequence RASQGIISYLA (SEQ ID NO:66),QASQDISTYLN (SEQ ID NO:70), RASQEISGYLG (SEQ ID NO:65), or RASQSISSYLA(SEQ ID NO:71); and the V_(L) region CDR2 has the sequence AASSLQS (SEQID NO:68), GASSLQS (SEQ ID NO:72), AASSLQR (SEQ ID NO:73), or AASTLDS(SEQ ID NO:67).
 12. The antibody of claim 1, wherein the V_(L) regioncomprises a V-segment that has a V-segment sequence as shown in FIG. 1.13. The antibody of claim 1, wherein the V_(L) region has the sequenceof a V_(L) region set forth in FIG.
 1. 14. An antibody that comprises aV_(L) region that has a CDR3 comprising GQYANYPYT (SEQ ID NO:57),VQYAKYPYT (SEQ ID NO:58), AQYANYPYT (SEQ ID NO:59), VQYSNYPYT (SEQ IDNO:60), VGYANYPYT (SEQ ID NO:62), VRYANYPYT (SEQ ID NO:63), or VQYLNYPYT(SEQ ID NO:64); and a V_(H) region that has a CDR3 comprisingX₁GX₂YEX₃FDX₄, wherein X₁ is S or G, X₂ is Y or V, X₃ is E or D, and X₄is S, V, or I (SEQ ID NO:38).
 15. The antibody of claim 14, wherein theheavy chain CDR3 comprises the amino acid sequence GGYYEDFDS (SEQ IDNO:43), SGYYEEFDS (SEQ ID NO:41), SGVYEDFDS (SEQ ID NO:44), SGYYEDFDV(SEQ ID NO:45), or SGYYEDFDI (SEQ ID NO:46).
 16. An antibody preparationcomprising an antibody of claim 1, wherein the heavy chain constantregion is hypofucosylated or afucosylated.
 17. The antibody of claim 1,wherein the antibody does not compete with ephrin AS for binding toEphA3.
 18. A method of treating a patient that has an EphA3-dependentdisease, the method comprising administering an antibody of claim 1 tothe patient in a therapeutically effective amount.
 19. The method ofclaim 18, wherein the disease is a cancer.